I think everyone needs to calm down. I noticed something from IGN's gameplay video #1 (X's and O's) that you may want to check out (link below):
1) In this video, the user runs a series of three plays within the span of 38 gameclock seconds. These three plays are either runs or completed passes--none of the plays result in the gameclock being stopped.
2a) Let's assume for argument's sake you had an entire game at 5 minute quarters where none of the plays from the line of scrimmage resulted in clock stoppage. In (1) above, the user was running these plays at a rate of 1 play per 13 seconds (38 seconds/3 plays=12.6, or rounded, about 1 play per 13 seconds).
2b) A 5 minute quarter game is total 1200 seconds long. If the player above was able to rip off about 1 play per 13 seconds, and assuming the cpu takes about the same amount of time, that would mean (again, given our hypothetical example in 2a above), that there would be about 92 plays combined--and that's if the gameclock never stopped.
Now, add in timeouts, incomplete passes, turnovers, penalties, i.e., anything else that stops the clock and you have an opportunity to run even more plays. From this observation alone, I'm led to believe that once everyone is used to the interface and calls plays like nobody's business, we'll get very close, if not right at, the average NFL plays of 115-120 combined per game.
3) Another observation from the video: during the 3rd play towards the end of the clip, the gameclock gets to about 4:13. The user at this time calls up his adjustment menu and calls an offensive line adjustment. While the user does this, the gameplay clock pauses while he's doing this.
Conclusion--the gameplay clock freezes when we're making/calling adjustments, which helps conserve time as well.
http://media.ps2.ign.com/media/776/776737/vids_1.html
Anyway, watch the video and judge for yourself. Based on my observations and the observations of those who have just started playing for themselves, I don't think 5 minute quarters may be all that big a deal since plays are run so quickly, and adjustments appear to freeze the gameclock. And, IMHO, quarter length is not important if the correct number of plays are being run.