I like having to use cover in shooters like STALKER. It's nice having to be tactical about it, so you can't just rush straight in.
In the case of Mass Effect though, and Gears of War and many other games that people call 'cover based shooters', it's pressing a button to hug a chest high wall that is almost guaranteed to block all damage while you wait for health regeneration to kick in. Pop out, shoot, take cover when taking damage, wait a few seconds for health regen, pop back out again, etc. etc. While in STALKER or ArmA 2 if you're crouching behind something you don't know if it's entirely safe, so you have to guess for yourself what you can hide behind, and health doesn't just regenerate.
The cover based shooting with health regen isn't that fun.
Ah, ok, misunderstood that then. I remember such cover mechanics from Alpha Protocol only, I think - and I considered them a major annoyance there. It was way more flexible to just take cover behind whatever you wanted to take cover behind, at a distance you wanted keep between you and the cover (in case of rockets and grenades), then to get glued to some piece of wall and have to waste time for the "take cover" and "go out of cover" animations to play out.