Ah, yes. So non-primary casters burn all of their WBL to achieve a less flexible and smaller range of abilities which primary casters get without spending a cp. It doesn't even bring them to parity, and then casters can use
WBL to widen the gap even further. Again, this does zip to deal with the gap in flexibility. Instead of Fighter McFighter being the guy who hits things, he's the guy who hits things and can also escape from certain types of magical or mundane prison a limited number of times.
Yep.
I can see a couple different ways to handle it. One would be to split things along class lines. Here's a rough, brief outline of a couple basic martial and skillful classes (note that skillful classes would probably be a mesh of this with other buffs):
Fighter: As a mainline fighter, they have this sort of progression for both their weapons and armor. They start out with more general improvements to make them more effective at whatever role they've chosen-the previously mentioned stuff that's roughly equivalent to item enhancements. When they advance, their choices channel into a path which meshes with the way they want to handle combat.
They're the generalist, a rough equivalent to the Wizard, with the broadest possible range of choices. You could make a rough equivalency between their specialization and school specialization; just as (ferex) a Focused Specialist [school] is exceptionally effective within that domain and less so outside it, so too would a Fighter who emphasized a certain fighting style. At higher levels, the available choices would mesh with the path the character followed. For example, a masochist would be hitting things like life-leeching, aggro-drawing (to borrow an MMO term), using their weapon to damage the WIS or DEX of their opponents (among other things) as a way of describing an attack which pushes enemies towards mindless aggression towards the character. Really high up stuff could be something like attacking the ability of enemies to perceive or comprehend the existence of anyone except you. So in short, stuff which meshes conceptually with how you built. A Knight would probably have something similar to a masochist Fighter, except with a much greater focus on their armor and resisting harm.
A Barbarian would be much more tightly focused on unstoppable force, aggression, momentum, &c. They'd be totally invested in their weapon. With a Barb, you might see things like the ability to batter through obstacles as if the character were adamantine while charging, destroying magical concealment, illusions, and protection (which in turn removes the pressure to get those things with feat trees and multiclassing), the ability to gain an assured hit in exchange for an assurance of being hit, being able to break through the barriers between adjacent planes with sheer force of will and a good smash, the ability to defeat death for as long as a battle continues, &c. You could also tie a lot of things to rage, make it less "You gain X stats for Y turns Z number of times per day," and more "You never need rest or sustenance while the target of your rage lives," or "Your other abilities gain power in proportion to the depth and length of your rage focused on a specific group or individual."
A high level Barbarian could chase someone forever without pause, destroying everything placed in their path as if it were cardboard. They might hit something so hard that it literally ceases to exist-not Critical Existence Failure, but rather a blow so strong that it is actually erased from existence, with this stretching farther into the past with the strength of the blow (if you've read Wheel of Time, think Balefire). If they grew angry enough and remained so for long enough and their target was a god, they might be capable of breaking into whatever plane that deity called home and attacking it until the god died, their rage was appeased, or their soul was destroyed.
A Paladin would be the martial counterpart to the Cleric in a truer sense. Their weapons and armor would channel the power of their god; as the equipment "levels up" its ability to act as a conduit would increase. At the point where it became sentient, it would either do so as a servant of the deity or as a direct link between the character and their deity. The abilities they'd have access to would be largely (and as they leveled up, increasingly so) linked to the nature of their deity.
For example, to use a very well-known god, take Pelor. A Paladin of Pelor, as they advanced, would have equipment which would allow them to channel Pelor's power directly, doing things like cutting away disease and injury, directly attacking the souls of Evil beings, gaining mindboggling strength (the Hercules example comes to mind), destroying the concept of darkness in areas, permanently or semi-permanently destroying the ability of Evil to exist in areas, things like Gandalf's trick with the light from his staff, severing connections between the Abyss and other planes, &c.
An accomplished Paladin might eventually be able to literally cut the evil out of people, strike the ground and permanently bar entry to Evil on a city-wide scale, briefly become an avatar of their deity and channel a large fraction of its full power, destroy the ability of disease to affect a crowd of people, or create divine lights which never dim or die and which burn Evil creatures which step within them.
A Rogue, as a skillful character, would not be as focused on their armor and even weapons as martial characters. Their advancement with their equipment would be as much about their movement and sneakiness as with the direct applications of them. A Rogue might, for example, gain the ability to scale any surface at their full movement speed with their daggers (treating them as adamantine while doing so), or to use their blade to widen tiny gaps into passable spaces, &c.
But again, skillful characters aren't just about weapons and armor. A Rogue would also be tied to their tools, both material and immaterial. They might gain the ability to (again, using something akin to the principle of contagion) poison a relationship, cut away at the ability of a bureaucracy or military to function efficiently, &c. They might become capable of 'picking locks' in conceptual ways, opening doors through solid objects, between planes and locations, or into the minds of people. They might instead develop in stages the ability to destroy the concept of their own existence to outside observers.
An accomplished thief might gain the ability to literally steal spells, taking them from casters and gaining them for as long as they wished, or doing the same to enhancements on weapons and armor. At Epic levels they might become capable of stealing from deities, gaining bits of power similar to those wielded by Clerics or Paladins. They might gain a sort of Shroedinger's Bag, where they could reach into their own bag and withdraw an item they know to exist which isn't directly held by anyone.
A more combat-focused Rogue might instead move through things like their armor ensuring that they can always gain the advantage, preventing them from being AoO'd while they are in range of more than one enemy or in another disadvantaged position, or while moving to leave such a situation. Higher up, they might be able to exchange positions with opponents. At very high up, you might see something roughly equivalent to Shiki's good old lines of death, where the Rogue can see precisely where to stab something to destroy its existence utterly (meaning an instant kill if they can land a hit).
Admittedly, skillful characters are difficult to fit neatly into that paradigm. But you might, for example, eventually have a Rogue who can reach into their own bag to retrieve a quill belonging to an emperor, and use that to wreak havoc and bring the entire state tumbling down in a matter of days or weeks. They might open a door into the Abyss and walk straight up to a demon above their CR and kill it outright with a single stab without ever being seen.
Archers. This might be a Fighter, a Ranger, a Scout, or who knows what. I'll lump it down here because it's sufficiently different. You might see things like curving arrows around obstacles in flight, pinning opponents together or to obstacles, &c. at low-mid levels. Shooting arrows, and later spells out of flight. Shooting gaps in AoEs like dragonfire. All as an immediate action.
Higher up, things like called shots on any object or part of an object or being, with relevant effects -- shooting out something's heart for a massive CON drop, calling a shot on a Lich's phylactery and treating it as a touch attack, shooting flames off of torches and lanterns from hundreds of feet away, &c. Later on, you could do things like Scry&Fry with arrows -- perfect sight on a target so long as they are known to the shooter combined with the ability to always deliver an arrow on target, even if it needs to teleport to do so, with a more advanced form for shooting between planes.
If the character is focused on speed, things like being able to fire one arrow at every target they can see in the same turn, or incorporating a better Flyby Attack+Shot on the Move into the bow's powers. If they are more precision oriented, things like those described above. If they're focused on power (say, a Fighter with a composite bow), something like the ability to shoot through any obstacle if they target someone or something on the other side. The ability to cause massive damage to structures, such as breaking down a castle wall or collapsing a bridge with arrows. For a mobility-focused archer (such as a Scout), things like being able to shoot arrows into things (advancing to include solid stone or metal walls, and eventually thin air) and moving on them (including jumps) as normal movement, even eventually including those shots as part of movement.
So an archer specced for speed and mobility might, for example, eventually be able to run along a path of their own arrows in mid-air, firing at every enemy they can see. An archer specced for power and precision could eventually bring down a castle by firing arrows at the keep or someone inside it, or assault someone from thousands of miles or a plane away.
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Obviously this is just me spitballing ideas and has at best a bare nod towards integration or balance, but you see what I'm getting at? It's all about being thematic and conceptual, making the abilities mesh with what the class is supposed to be like, and what the character specifically is aiming to be. A lot of the higher-end stuff sounds sort of absurd and superhuman, but when it comes down to it that's what high level characters are. Casters express that through utterly bullshit magic and massive flexibility, martial classes through absurd feats of skill with their weapons and armor, and skillful classes with obscene competence with their skills and talents disassociated from both magic and (somewhat) weapons and armor.
The biggest issue is with skillful classes: they aren't really casters, and they aren't as closely tied to their weapons and armor in many cases. I partially addressed that by including tools. I suppose it might be better to just come right out and tie a lot of it to their skills.