I’m sure I’m not the first person to suggest this, but here goes:
It doesn’t feel thematically right for invisible characters to ignore trap effects. When I watch my opponent make a trap tile match, trigger an ability, and then just walk away from it, it doesn’t sit well. When I’m actively trying to hit an invisible dude, it seems reasonable that s/he could dodge it. When that dude blunders into a trap, it makes less sense that s/he ends up walking away unscathed.
If we want to be a little nerdy about it, consider the major traps in the game right now: Fury’s Demolition and Daredevil’s Ambush. Explosives don’t care if they can see you or not, and Daredevil is like the first character to show up on my list of superheroes who can still hit you when you’re invisible.
The easiest fix would be to make it so that invisibility only protects you on your opponent’s turn. That way you can still invisible your way through Daredevil’s self-activated ambushes, but not evade his crotch-kicks when you stumble into them.
Again, a lot of this stems from my gut reaction to watching invisible guys dance around traps–it just feels wrong. Maybe it would make traps too strong and invisibility too weak, but it seems like that balance is oriented in the other direction right now.