As a long time Scaper I am no stranger to the benefit that special abilities or skills bring to a board game. A large part of Scape tactics come about from selection of units with complementary skill sets or units that may give an edge if the luck of the d20 is with the unit commander. In a tabletop skirmish game skills are awesome. The basic version of Scape has no skills and it sucks like a nuclear powered Dyson. No, in a tabletop game skills are that all important edge that makes an extra bit of fun for participants.
So I imagine when Monsieur Gygax was thinking about D&D the idea of dropping skills from the units was anathema and I can understand the point of view. A wargame or similar with no unit-specific skill matrix is yawnsome.
To further expand on my Scape example a Scape figure has five major ratings, Attack, Defence, Range, Movement and Life. A skill gives some advantage that increases these ratings either permanently or given some random event or particular set of circumstances. There are angels with shields who automatically double their defence. Furious samurai who can add to their attack when they engage the enemy. Gorilla soldiers who can move twice as far while the cat suited secret agents are on the field.
The reason this increases the fun in wargames is that the game runs within very strict rules and the number of outcomes to a particular scenario, vast as they may be, are finite.
Now let's make a sideways move into role play.
My favourite skills system ever in a role playing game is the Over The Edge system, where you basically make up your own skills and get dice pools in them. There are skills that a lot of people might have like "fighting" and then skills that people might not choose like "make up artist". The joy of it being your character can be good at whatever you like.
Of course this case is all a matter of scope the number of situations that could arise in RP are vast compared to the number of situations that could come up in a skirmish game. The chances that a general amnesty could be called in a skirmish and that because it's christmas day the characters will engage in a pleasant game of footie are slim to fat. It's not part of the game's scope.
Set a scenario in a WWI trench on christmas day and watch what happens. Exactly.
The immediate reaction of the role play scenario creator to this problem is to start mucking about with "skill trees" and the like. I don't know why any human being starts thinking "I can taxonomically record every skill a human being could ever need" or even "other people will find rooting around in my taxonomy fun" or even "this hideous conglomeration of number soup will be the one thing that makes the game worth playing". I'm not sure anyone does think the last one. In fact I think that people probably don't even regard them as a necessary evil. They might get as far as necessary but evil?
Evil can mean a lot of things. When you're trying to play an RPG evil is anything that turns the game into a laborious time waster. So I think large skill trees certainly fit into that most of the time.
Note here I'm not talking about suggested skills. Having a vast array of contextualising information about the kinds of skills one might have is not a problem. Especially not if your skillcyclopaedia indicates the proper definition of all skills should be agreed between Host and Player before play commences. Remember the player wants the coolest persona that won't break the game and the Host wants to provide the most thrilling experience into which the characters fit like perfect players in the dramatic events of the story.
I've never met a player who wouldn't agree to prune the power to feel more like they fit in the world. Power gamers tend to be caught in a well intentioned attempt to cover all possible bases. Power Game characters tend to lean on their magic character stat though and this makes for a one-dimensional character most times.
I've never come across an RPG where the variety of skills available was particularly what made the game in fact I've never seen one where telling the player any finite number of skills is all the skills that exist is anything more than a massive bummer to the players.
If you want to give the players a menu of skills and say get on with it you're not Hosting properly. The skills a player may or may not need in the course of an adventure or campaign should always be a negotiation between player and Host and should never come off a list.
That's how I do it, that's how Over the Edge does it, and it's worked out pretty well so far.