What if you are +0? You can't store passion. Do you just gain a level in the skill automatically?
I'm uncertain what to do if you exceed your max passion. Particularly in the case of going from +0 to +1, I'm tempted to apply it retroactively to the action. Main problem here is that the player doesn't get a chance to specify, and in testing I kept thinking of the action normally before realizing, oh yeah, I have to apply something fancy to it. Not my first choice, but I don't have a better one.
For having a limit and exceeding it, I'm torn between the additional point being spent retroactively and all of it being spent at once. The former is probably mean, though.
In any case, yes, +0 to +1 requires 1 Passion, as does +1 to +2.
One immediate solution that comes to mind is to remove the requirement for spending passion to gain levels in a skill: you just always have a flat [1 / Current Level] chance to level up, and you will level up at twice the speed considering you go from a 50% chance to get a [1 / Level] chance to level up, to a flat [1 / Level] chance.. I think this makes your system less unique, though, and it takes emphasis away from that one decisive roll. So I would avoid this if I could.
It's also unfortunate in that a lot of skill levels require a separate roll. 1, 2, and 3 are fine, but 1/4 and 1/5 don't map directly to a d6. Needing to roll a separate die every time someone uses a +4 skill would be obnoxious.
What if you get +1 additional passion if you roll 1 on a passion-action? Or perhaps just double the passion you get from passion actions. To keep players from simply spending 1 token passion on every action, you could force players to use ALL passion on an action if they specify a passion action. Takes away a bit of player agency, but it cements a sort of theme where "passion knows no bounds" or something.
I did consider just giving 2 Passion per [1][5][6], but as you suggest it statistically allows players to spend a Passion every single turn, which detracts a fair bit from the special-ness. It also plays oddly with the lower levels, since you go straight from +0 to +1 and 1 Passion to immediately boost yourself to +2. From where you go immediately to 2/2 to boost yourself to +3, where you go straight to 2/3 and then to 4/3, unless you spend at least a point in the interim. Feels odd and chunky to me.
I could indeed force them to go whole hog if they're going any hog to deal with the passion poke thing, but you can still spend it as you get it so I dunno how much that'd change things. Plus everything would be in multiples of 2, which would be odd.
A related idea would be forcing players to max out their Passion before spending exactly that much, but I feel like that reduces agency more than I'd like. If you want to spend as much Passion as physically possible in one swing, that's fine. If you don't, I feel like you should be able to do smaller projects and only spend what you think you need.
How about this for classes?
Definitely interesting, but I'm concerned about players putting all of their skills into one class, or just neglecting anything they can't fit in there. I guess I could try to scale it so that putting more skills into a class required more total expenditure to raise the class (eg Soldier: Swords Shields Cooking is easier to level than Archmage: Every Magic Skill), but then I'd need to fine-tune the benefits of every possible number and level of skills to be balanced with each other.
Another option I like would be applying special abilities to class clusters, so you'd have some incentive to keep skills linked by some rationale. Maybe Swashbuckler has a Sea Shanty ability that improves Swashbuckler class skills on the ocean, so you want to keep your ocean things and only your ocean things in there, while Chaplain blesses targets of Chaplain class skills so you want to keep your supportive stuff in there. But then Swashbuckler becomes an ideal class to put Fishing and Chaplain has no reason not to gain Cooking, so maybe not.
Another thing I was thinking of was allowing you to combine skills, such as using Necromancy+Fire Magic to create flaming zombies. I could potentially limit such combinations to one per class, so a Druid (Life Magic/Plant Magic/Animal Taming) couldn't use both Life and Plant magics to grow plants at the same time, but their knowledge of Life Magic would improve their knowledge of Plant Magic. On the other hand, this would make "custom" classes ruinous; a Flame Priest could never use both his awesome fire and awesome divine powers at once, so ideally you'd want each class to have a "main" skill you actually intend to use, and at least two filler/utility skills you'd like to get stronger with your main skill, but would never consider using together with it. That's... probably not what I want classes do be/do?
As seen here, relevant informarion is shown on the left (+bonus from class, class name, +bonus of skill including class bonus, name of skill) and useless stuff in the middle (level has no effect separate from bonus), then passion on the right where you can skip to it.
Sometimes it's the little things; that formatting is quite good.