The most simple suggestions are the most accepted, I'd say. Especially if it involves work on the devs part. The simpler the work, the better chance to have of implementation... So, here's mine-
This would be considered an inherent power to everyone. Instead of a recharge timer, institute a 'charge bar.' (Think Domination for dominators). This way, the signature move can only fire off for a set duration (or as a massive, built-up attack, as most 'super-moves' are), and after the player has been involved in fighting already. This would include toggle powers like powerful (but limited duration) shields, the super powerful AoE heal, Ranged debuff AoE, or whatever your little heart desired. The point system could be modified so that the more powerful the signature ability, the longer it would take to charge (as well as lose charge, or 'decay' out of combat). When the move was charged, it stays charged, and you pop it off whenever you like. This would ensure common and widespread use in PvE, ignoring the insane cooldown times and instead allow players to use it 'as needed', avoid spamming outside of combat, and give something for players to 'look forward to', plan for, or even save up for in difficult encounters. You would have to define how it charged, say, taking damage or dealing damage, or having friends take damage/deal damage, but the bar would certainly have to charge faster for PVP encounters.
However, if it was a toggle power, it would have to be for a limited duration for balance issues. Also, if you chose damage types or abilities outside your power sets (for example, NRG/DEV blasters choosing a psionic attack, or tankers choosing a sniper attack or heal-other ability) it would increase charging time.
I'd also say holds wouldn't remove self-buffs for this, but self buffs would be for a set duration (I'd play the starman theme!) cause you'd hear the tankers, scrappers, stalkers, and brutes really weep if they popped their ultra-shield and got hit by a sleep move for 20 damage a half second later. I'd also say that the signature power could not 'contradict' your power set, for example, an invincibility tanker could choose nothing psionically based. This is for exploitation issues, because you KNOW there are going to be people that make massive buffs against their hated damage type of choice, and throw off the intended balance that the devs put in place. It'd make PVP even more of a nightmare, with how creatively people exploit the costume system- imagine something that powerful game mechanics wise in the hands of all those silly players.
I can already see a number of blasters grabbing super resistance shields, tankers making spammable self heals (in ADDITION to what they have already) or 'break free' effects, and stalkers making a second form of placate.
However, I can also see tankers dropping a damage shield on squishies, scrappers whipping out a PBAoE heal on his tanker buddies in range, and having the OTHER tanker throw a sniper attack to nail the runner or grab a boss' attention.