Hmm... I'm just curious, because I had a different question that MAY be similar (or might be completely wrong).
I haven't checked this, but here's something you could try (involves both scripting and eventing):
Make a new actor and make a characterset of the skill icon (4x longer and wider than the regular icon). Give the hero the characterset, and call it "Skill", or whatever you want (you can leave it blank too). Now when you want the player to name the skill, use "Name Input Processing" for the actor.
After that, you can try this bit of code. I haven't tested it, so it might (prolly) won't work, but here goes anyway.
$game_skills[x].name = $game_actors[y].name
Replace x with the ID of the skill, and y with the ID of the actor. Hopefully, if Enterbrain was nice enough to create all these shortcuts for us in Ruby, it'll work. :thumb: