Honestly if you give any character customisation potential they will probably end up overpowered anyway. The most likely scenario is the player will take their Jack of All Stats
main character, pick a specialty that suits their playstyle, and stick all their skill points in that area (as an example, a player who wants to specialise in physical attacks puts all their points into strength). The only way you'd get around that is to cap the MC's stat growth, and your players will probably not like that.
If you need some examples of great games that cast the MC as a blank slate for the player to customise, look no further than the Shin Megami Tensei
games. Nocturne, Persona 3 and 4, and Digital Devil Saga
1 and 2 all start out with the main character as a Jack of All Stats
. By the end they are normally far and away the best character.
You aren't really going to get around this. The main character is the player's avatar in the game world, and the one through which the story is being told, so it's natural for the player to want that character to be powerful, especially if they cant be switched out. If you try to force the Jack-of-All-Trades
template, players will likely react unfavorably.
About the only way I can see around the problem is to not have a main character. Case in point, Final Fantasy XII
has a nominal protagonist in Vaan, but the hero is obviously Ashe, and Vaan's use is never forced (except at the beginning when he's your only character). When I played it I ignored Vaan entirely and treated Ashe as the main character, and I never felt like the game was forcing the choice of protagonist.