I don't think it can really break gameplay.
And it can bring on lot more strategy , like having to use another way to reach someone using cover. Or the use of grenades also !

I played Uncharted 2 and it was great just great and fun with the cover system, and the gameplay was really fast and furious.
You can't hide a lot when people have seen you or your gun fire

Even better make deeper gameplay :
with destroyable cover objects, less or more destructible by grenades, fire power etc ...

Well , keep it up !