The trick was always balance. If a custom hero is too strong it just becomes boring. It ws easy enough to set your own limits on hero powers.
I always found having your hero a bit weaker than the strongest bad guy was always more fun. Alternatively, having a medium strength hero come up against wave after wave of weaker villains but giving him/her a finite resource of energy that had to be recharged (I think it was called energy X or something) meant that there were times that called for a more survival based strategy rather than just out and out wham, kapow, kayo