I think it's important to think "What behavior do I want to encourage" and "What behavior do I want to discourage" when designing a game. For example, if you're making an RTS and you want to discourage micromanagement...well, you'd need to remove any game benefit to micromanaging stuff.
One of the ways that Nethack keeps the game interesting for lower level characters, is that the loot and random stuff you can find varies SO WILDLY. Pretty early on you could suddenly just find plate armor, or a Potion of Gain Attributes, or several spellbooks that you can't quite use just yet. It encourages the player to search around a fair amount, or at least not rush... but at the same time, if you find a sink, you very quickly learn that playing with it will get you killed remarkably quickly except for the one in thirty chance that something great happens. The player is discouraged from experimenting with the unknown when they are doing well.
Nethack encourages newer players to say "Hey, what does this button do" because, while everything is very deadly, it's also frequently very amusing to die to--and just sometimes very helpful. "Oh god, I didn't think that could happen!" is kind of fun when done right, and even more fun when it's escapable. Players learn that gaining knowledge really helps them out in the long run. Still, as previously noted, if knowledge is TOO obscure then players might not bother trying to find it themselves anymore.
Because loot can drop so randomly, they kind of have to keep players from sticking around in one place forever early on, trying to farm Wands of Wishing off jackals and goblins. Limited food is annoying, but it's a good way to discourage players from staying in one place. Also, the occasional out-of-depth monster means that once you've been sitting in one level for a while, going deeper often makes you safer. The monster generation tables being based on dlevel AND character level similarly keeps the player going forward, since hanging back just isn't even all that safe.
For the early and midgame, the wide variety of equipment and the small number of (important) class features discourages people from trying to play the same build every game. You can encourage playing a more predictable game by giving less random equipment and more important class features...but in a roguelike, balance from game-to-game is less important than keeping player interest, and Diablo isn't THAT fun. (Balance between classes is still important, but hey, it's one player, it's not that huge. Game-to-game balance is kind of important to skew a little, so the player never knows when they're going to win big!..just as long as it's often enough to be fun, and the game isn't unfun when unlucky.)
Lots of roguelikes have a weapon specialization system; ADOM's is more hardcore than Nethack's. That specialization system discourages players from swapping weapons too often, and it lets you give the player more good equipment for the same balance (what good is a wonderful sword to an epic mace user, well, that becomes a tough decision). ADOM's is farmable though, since it's safer to go to weak places than in Nethack. Nethack's is more strategic, since you can only even HAVE so many weapon skills. This fits their styles, though...ADOM likes long-term characters that play it safe, Nethack encourages more dangerous play. Keep in mind what you're encouraging before you decide on a skill system: If your gameplay can't support long-term games, you might not want to encourage players to farm when it won't be fun.
That actually has some relevance to Fenrir's game. Think about what an "elf throwing" skill means. It means that if you've thrown very few elves, you have no good reason to start; you'll probably miss. It also means that if you've thrown a ton, you might as well keep specializing. You're discouraging the player from branching out, and maybe making the game unbalanced in favor of elf chucking at the high end. If you want to encourage the player to throw elves whenever convenient, you might not want a skill for it--instead, consider making it just based on level, strength, dex, etc!
When do you want a player to throw an elf? If the answer is "whenever melee won't reach far enough", well, you'll want to make it easy enough for melee characters to get into, probably without practice. If the answer is "whenever I need to shoot a dragon, but I've run out of projectiles", then you might want to base it off a more generic 'throwing' or 'ranged' skill. If the answer is "for laughs, because elves are weak and easy to kill", then mages need to be able to fling elves too. If the answer is "for massive damage", then players are going to spend hours herding elves into the room with the dragon, or making the dragon follow them into a room with elves, or elaborately constructing walls to channel where critters are. "For defense when the elves close in"? Then you might build elf throwing into a wrestling skill instead, where the player can specialize in a skill that lets them do less damage (due to being unarmed) but has more defensive options (elfchucking).