Most importantly - give cover its own button -Triangle is the best option (L2/R2 = sprint/grenades) and make roll another button.
Entering cover needs to be faster, more fluid and less likely to get you killed - better animations which keeps you more protected and with less lag.
I think rolling into the cover instead of gliding into it would help since you are more protected behind waist high cover when rolling, where as you are not protected at all when you glide into it like you do now in UC3(glide is laggy also). In UC1 Drake rolls into cover.
Exiting cover should also be faster and more fluid - it should not be as sticky as it is in UC3.
UC2 has much better cover overall (people should check it out) but it could and should be even better again for UC4.
I'd personally like it if when I was at an angle where I could see somebody, my bullets would count as hitting them. What they did with only snipers being able to headshot people from certain angles seems tomhave messed things up, so that you can sometimes get to an angle where you can see a fairly large portion of your target and yet your bullets won't count as hitting them when they clearly are.
you know what, i actually like the cover system in uncharted 3, sure it has it's flaws but i much prefer going into cover being somewhat of a struggle while in a gunfight then having people being cover dependent (overuse the cover system, like they use grenades nowadays)