Just a couple of things...
I hate it when I get a 15 yard penalty and I look over to see my entire bench jumping up and down like a bunch of idiots. Not to mention half of them are jumping up at the exact same time.
I agree that there shouldn't always be a sold out crowd. I was playing a UCF dynasty in which I played a FCS team, pouring rain. Not an open seat in the stadium.
I hate the FCS thing. Just take the time to put some well known DII schools in if your not willing to put them all in, no one likes having a 70-0 win over FCS East Lizards to boast about.
I'm really starting to like recruiting, I like the option to quick call, so in 2010 I would like to see more of this. Also I don't like recruiting an OLB and then him coming in directly as a LOLB, I know this is subtle because it is so easy to change, but there is no reason they shouldn't be put under a list of just Linebackers.
In my OD, I moved a power back with 84 speed over to FB because I knew he would be the third man on the Depth Chart for as long as he was there. His speed changed to 68... Why? He didn't gain weight, as far as I know his strength did not go up, so why the decrease in speed? And why so enormous? There should be no reason for this.
Along those same lines, I can't tell you how much I hate it when I'm 4 deep at OLB, and only 1 or 2 deep at MLB, so I make an attempt to move an OLB to MLB and once again, he will fall from about a 80 to a 70, in one position change. The main difference here should be learning the position, and that's why if we are willing to make the move in the off-season, we should not be punished for it.
After messing with the sliders a good bit, I've found good gameplay, good stats, and close games where there should be close games. The thing is, the way this will happen is I'll shut down previous plays for maybe 2,3, or even 4 yards and then BAM. In order to have both a realistic and a competitive game against the CPU, they seem to have an odd number of 35-70 yard plays. This works for me now, because as I said I get a realistic set of stats, but by next year I would love to see a coupe games a years where the offense beats me through first downs.
Heisman... We all know robo QB is a problem, I'm just asking that next year we loosen up on the coverage a little bit (therefore decreasing the picks), and drastically lower the way the CPU throws the pall on the money 90% of the time. Also I wouldn't mind if maybe the CPU didn't have eyes in the back of its head.
As everyone else has already said, let's see some Refs on the field, as well as a chain gang. They spent so much time on the cheerleaders and Mascots (Which are constantly break dancing on the opposite side of the field, even if their team is down by 50 points), that they took certain things like this away from the hardcore fans. Also, I'm getting sick of seeing the same Ref umpire my game, lets throw some variety in there.
Basically the same thing as above, but would it hurt to see some signature coaches? I don't know as to the rules of paying college coaches for things like that, but they have coaches in Madden right? Names and all? I would love to see Spurrier walking down the sideline then throwing his visor to the ground in anger, or possible Tressel with his old school style attire.
The Playbooks are sort of a love-hate relationship for me. I'm a Gator fan, so seeing the Gator Heavy is always cool, and using the South Carolina playbook is awesome, but I get to a point where after you begin to use different formations, your seeing the exact same plays, except with a different formation, and a slight variation on the name. Running plays work for me, they certainly have enough to keep a game original, but the pass plays... I'm just sick of running curls, slants, PA rollout.... After reading the money plays article, you can tell I am clearly spoiled with the generation of gaming

.
I wouldn't mind seeing some pre-game stuff, I always hate hearing Kirk talk about "If you haven't heard about this young man yet, you certainly will today." Pause 5 seconds... "And now lets go down to the coin toss, where well get ready to kick of today's game."- There's your pre-game.
This is possibly my biggest problem with NCAA Football, and it is probably the least likely to ever get fixed. When I'm playing a Michigan State-Northwestern game, the same week OSU is in Ann Harbor taking on Michigan, I DONT WANT Lee and Kirk to be at MY game. Now I know how difficult it would be to get a variety of announcers for one game, but it always has me thinking, what if they just grabbed 5 or 6 other announcers, and spread them across the games that should be telecasted? I know that Verne for CBS does the SEC (and this is all theoretically speaking, as I know that EA would never spend the money), what if Verne did the SEC game of the week? What if Brent Musburger did the late night showdown, typically College Gameday? And then for your others, why don't they use either lower ESPN announcers or even broadcasters from networks like Raycom, and Comcast? It just seems that that would add the life to college football that everyone is looking for, but once again, it's hard to tell if EA would ever spend this kind of time and money for something casual gamers don't typically care about.
Obviously D-line/O-line needs some fixing. It would be awesome to see a casual linebacker blitz not picked up by the O-line. Also, is it possible for the QB to roll out and still actually pass the ball? I've noticed that every time the opposing QB turns on the jets, it's only to get big it 3 seconds later.
CPU running backs need to be smarter. When there's a hole, they need to hit in, not juke into the opposing D-line. When there isn't a hole, they need to either fall forward for yards, or try to juke around the defender to make a play. Not run sideways, or backwards.
After game celebrations. If Oregon State beats USC, then their fans should be ready to cover the field. If my team wins the National Championship, I'd rather see confetti falling from the sky, then hearing "And that's gonna do it folks, Michigan state... 21. Oregon State... 17" I wish maybe a little post game analyses would come after games. Maybe even have sort of a Gameday thing like 2k8 NCAA basketball does?
Online Dynasty made this the best NCAA Football since '06. Lets keep that for next year, pan out the glitches, and take into account everything everyone has said above me, and including me, and you will not see a happier bunch of fans than those who play NCAA Football 2010.