In 3E I always allowed my Rogue PCs to drop sneak attack for more skill points and improvements in trap finding etc.
This is part of the problem. The notion that you have to drop combat ability to gain non-combat ability, or vice-versa. It's... silly.
If you simply say that every character has 5 non-combat 'slots' and 5 combat 'slots' and separate feats or whatever mechanic is used into combat/non-combat and not allow swapping, then everyone is on an even playing field and can choose what direction they want to go in. You could still have classes but the classes just give bonuses to certain things rather than pooling combat/non-combat together and adjusting the ratio between the two for balance.