Well more or less similar ideas were already in i could bet, but still, if we have support perks, which wouldnt be taken normally, but are gained free for quests/dialogues etc., why dont we have support skills on which no one spends skill points normally, so that people could get by some other way, of course the gain could be limited, and you couldnt raise 300%, but you could raise your skills to let say 100%, i think it would be fair, and it could help characters be flexable and more all around, so less alting would be needed.
how skills could be gained?
Well, there could be different ways, or a mixture of them all, for example:
1. Skills could be gained by doing something that belongs to skill. Science would increase when you science items, for example ten items could raise 1%. Repair would increase when you repair items, steal when you are stealing something etc, first aid when you are healing someone, gamble when you are gambling and etc.
2. Good old fallout2 way, skills could increase when reading books.
3. Doing some quests, that would need related stuff, for example repairing water pump in boneyard could increase repair skill etc.
And maybe you can suggest some other ways