That is a large problem in general. It does not matter what the speed ratings or even man coverage rating is, CBs are able to back pedal nearly as fast as they can run. It has improved a bit over the years though.
I'm not sure about the speed and coverage issue though. I have seen slower corners keep up with fast WRs on go routes, but that was because they got the position. But they get beat often enough to where if I see Torry Smith 1v1 with a slow corner I take the shot. To be honest I think the game does a good job on that front.
The problem I have on deep balls is two fold. First is an issue EA is addressing and that is passing accuracy. I either hit my guy or miss horribly. Second is the amount of ints on those matchups.
On other routes speed does not matter quite as much. A slow CB with 99 MCV should be able to cover the WR on most non vertical routes (ins, outs, comebacks, etc). Drags routes should be a problem, especially if it has pre snap motion. And for the most part I don't have any major complaints in that department.
I think with the new Madden I may run some tests to see what impact agility and acceleration has on the WR/CB matchup. In my opinion those two should matter much more than speed.