I've been brewing a CoH tabletop system myself, and BOY is it hard work!
My biggest "mistake" so far (that I refuse to fix) is that I wanted to introduce a stat system (Your basic STR/CON/DEX etc sort of thing), and have each stat be useful in some way in combat: Power (strength) increases damage, Perception (Wisdom) adds to attack rolls, Agility (Dex) gives a character a defense bonus, Toughness gives some resistance to all attacks, and Intelligence and Charisma affect Buffs/Debuffs and Controls. And unfortunately, between all that and enhancements, the gulf in power between any two same level characters can get pretty big. Also, it doesn't scale well, especially in a D20 system. Like, +1 damage at level 1 is significant, but at level 50 (assuming one doesn't ever invest in increasing that stat)? Not so much. Also, a few points of resistance is no big deal for a Tanker, but for a Controller, it's HUGE.
So I've had to put hard limits on things. Part of the issue is that I'm trying to keep the stats and the bonuses they give 1:1. So if a character has a Power of 3, they get +3 damage to their damage, and +3 to any kind of strength check... Which in and of itself is an issue because how powerful your mental blasts are doesn't necessarily translate to being able to arm-wrestle someone, but mweh. Though I run into issues where I don't want Blasters to out-control Controllers or out-debuff Defenders just because they put a point in the relevant stat and tossed a debuff enhancement in their power, but I don't want to make their controls and secondary effects so weak as to not be worth using. HOWEVER, I also don't want Defenders to absolutely melt things at level 3 or for Controllers to have unbreakable mezzes that last all of combat, either. One thing I've done is made it so that your stats can't give something a higher bonus that it's base amount, but you're still talking about doubling the effectiveness of some powers right out of the gate.
I mean, take Dark Blast. Giving a foe -1 to hit is fine. But -3 after stat buffs and a single enhancement (assuming enhancements give full round numbers and not fractions...)? Do I allow that to stack? Currently I only have a chance for debuff occurring on Blasters, but for Defenders who start with a higher base number, that can be up to -5 accuracy after one attack and that's just disgusting. Also, it would eventually be NOT fun. Like, in a video game against NPCs, it's no problem to lay down a few mezzes and debuffs and go to town, but what does a real live GM do to challenge their players and keep them interested?
And then there's the bookkeeping. Keeping track of endurance and what powers are on cooldown/recharge is making the use of "power cards" a necessity, but at that point I might as well be designing a CCG instead of an RPG! Not to mention the sheer NUMBER of powers and abilities one gets access to later on... just contemplating what a character sheet would look like is giving me a migraine!