Alright... Just to make things clear, cover 2 only refers to where the safeties play. They play 2 deep zones. Cover 3 means that you're now releasing a DB to play a 3rd deep zone... None of these mean that you should have anyone in the flats, so saying the generic cover 2 and cover 3 will stop the flats is false. The Cover 2 and Cover three are simply terms used to describe the safety play. As an example look at the generic Cover 2 in the 43, you'll notice that the two DBs are playing a flats zone, somewhat, and they should be playing a press, which to the best of my knowledge, it looks as though they are. This should slow down a screen just fine, it does for me and I generally play as a DE or DT to start. But it doesn't STOP it, it slows it down. Cover 2 Man Press works better to stop the screen, but it leaves the WRs a bit less covered.
Then if we go to a generic Cover 3, we see that the DBs are now dropping out into deeper zones, while the LBs cover the flats somewhat. The problem is that these are LBs and not generally the best cover guys, so it's a toss up if it works or not... The best bet to beat the screen is Man Press, or Cover 2 with the additional press before the snap. That and being aware enough to know that if it looks like you're getting to the QB to easy that you're getting set up for a screen should be all you need.
After that, there are all kind of containment plays in the 43 defence... I think most playbooks have over 30 plays in there. The containment options are all there, but you have to know your playbook to know what works and what doesn't...
But to simply throw out Cover 2 and Cover 3 is rather funny since they're just generic terms used to again describe the Safety play. As an example, you can have the Dime Cover 2, where the flats are covered, or you can have the Buccs/Bears Cover 2 with the MLB dropping back into a deep zone. But in the end, they're all cover two plays because of the safety play... Just like Quarters means that All DBs are dropping back splitting the secondary into 4 parts...
So with all of that being said, a known issue with the 2k series was that the screen passes didn't work at all since the only way you could get the ball to your back was to lob the ball to him... Trust me on this one, if you look up my other posts you'll see that I'm a huge 2K5 fan, but I admit where there were issues in the game. And when you add in the fact that the screens didn't work, and that they set up their cover 2 a little different, it isn't even a fair issue to discuss.
This entire "screens plays work too well" is all spurred from people playing poor D and exploiting the insane blitz plays in this game, resulting in players simply throwing short... End of story on that... If there were things that could be done against the blitz other then short passes then players would do it, but if you do anything more then slants and screens you get sacked... A lot of the time I see online guys play blitz for two or three downs and expect that like magic, the only time they play a zone or man, they're going to get what they're after. It's a joke and shows how many players rely on the blitz... Because 9/10 if you play against a player who doesn't know how to counter the blitz you're getting your sack. Logic like that results in players expecting that 9/10 times that they play a zone they'll stop everything that comes their way which isn't sim or realistic... It's just sad.
I'm not a huge Madden guy... I'm no genious, but I know football.
P.S. Also, as an issue for the 2K5, 2K allowed you to move your DBs in or out, as well as up or back, which would help, but that's not in this game, so it can't be used as a fix for this year...