If I'm not mistaken, when picking your uniform in the team select screen, you can only choose plain white or plain black cleats.
I think the logo slots work all right. I think though that for the chest and pant logos, instead of being forced to use either the primary or the secondary (keep these options), we should also simply have the option of various equipment sponsors (that are already in the game). Maybe I want to use two logos, but I also want to put a nike swoosh on the right shoulder or on the pants.
I should be able to choose whether I want primary or secondary logo for the midfield and sideline logos. Maybe I want an empty midfield but the primary on the sideline. But I want to keep the primary as primary because that's the symbol I want to primarily symbolize my team in the menus and on the score ticker at the bottom, etc.
White and black should remain default options for cleats and socks, however, I'd like to be able to pick a 3rd color for each (as there are plenty of teams that wear colored socks...and how come there aren't any solid cleats that aren't white/black). Along the same lines, a third pair of pants would be nice.
Also... instead of "Primary," and "Alt," the pants should be (including my wishful thinking 3rd set) "Home," "Away," and "Alt." Some teams wear the same pants home and away, but not all. And while you can set up the alt pants as your "away" pants, it you still have to auto-select it, and while I can do this for both my team and the other team (in the case of playing against a CPU controlled teambuilder team) for offline dynasty or play now, when playing in ONLINE dynasty, I can't control what the other team wears. Home, Away, and Alt pants would fix this.
Pants stripes that line up with jersey stripes. How hard is this? When I create teams, I never use stripes on both the pants and sides of jerseys (that continue down to the waistline) because NONE of them seem to match up. Even if they match-up in teambuilder, they don't seem to match up in game. Also, the stripe/logo relationship when it comes to logos on the side of pants doesn't quite match right. I tried making a pair of pants with a logo on the stripe, but what came out in the game was a pair of pants with a logo about 2/3rds on the on the stripe...it looked silly and amateurish.
Pride stickers. Whether as default options, like they were before...or as an uploadable logo (preferably a 3rd slot).
Helmet numbers -- Fix them. If Teambuilder shows them Bama-style, then the game should show them Bama-style. But Teambuilder should also include some options for putting them in other places, such as on the front or back, like many teams do.
Helmet text. Many teams have text in the white areas on the front center and back center of their helmets. Some may even have images. Arkansas has "HOGS" written in the white part just over the facemask. Doesn't Texas have their longhorn logo their? These options should be in teambuilder.
Leg-text. Oregon has it, and while I'm pretty sure they're not the only ones, I can't think of any others off hand.
Better helmet graphics. If no where else, uploaded graphics should be movable and stretchable on the helmet. I know many people would like to create the more unique looking helmets like the Philadelphia Eagles. This is hard (impossible?) to do without being able to move or adjust the size of the logo.
Yellow home jerseys. I know that you can accomplish this with some trickery, but the fact of the matter is that it requires trickery. Southern Miss has a good yellow color that's used as a home jersey. But Central Florida's gold jerseys look practically white and they get away with those as a "colored" jersey, forcing the other team to wear a dark color (meanwhile, in the NFL, when the Patriots wear silver at home, the visiting team has to wear their colored jersey--though in real life, UCF wears gold with opponents in white...so maybe the biggest problem is how light UCF's jerseys come up in the game).
[On a related note, do LSU and Georgia Tech default in their white tops at home?]
[On another related note, the NCAA has changed the rules and now allow the home AND away teams to both wear color jerseys as long as the colors are very different. When will NCAA Football be updated to account for this rule change? We saw USC and UCLA both wear colored unis in a game recently, and another EA title, FIFA (soccer has different uniform rules, but still) allows both teams to wear whatever they want...so it's not like it's a question of programming...not that it would be.]
Perhaps the ability to select one teams OFFENSIVE roster template and another teams DEFENSIVE roster template. Maybe I want to roll with Georgia Tech's triple option offense (and as such, their offensive personnel), but I don't like their 3-4 defense (or the personnel they have which are more suited to play 3-4).
Just to add to others suggestions:
Pipelines, definitely need to be chosen.
Stadiums, customizeable...and upgradeable. If I want to build up a program, it's most realistic for me to start with a 1-star school with a small stadium. What's unrealistic is getting invited to a big time conference, hitting 5 or 6 star prestige, and then playing at that level for 40 years... and still be playing in front of a small home crowd of 25,000 or whatever size you started with. Regardless of whether or not it is applied to regular teams, with Team Builder teams, I should be playing in an entirely custom stadium, and at points throughout my long dynasty, I should be given opportunities to expand the stadium. The change would not only effect max attendance, but also athletic facilities rating, as well as be a visual upgrade. I'd like to pick where the visitor section is...the student section, etc. etc. etc.
Rivals. I definitely need to choose these. Maybe I want to replace EMU in my dynasty because they're the worst team...but I don't want whoever is EMU's primary rival. I should be able to select a certain number of rivals, and perhaps select which is the primary rival (for the coach's goal that sometimes pops up to beat certain rival). And it'd be nice to name the rivalry game also, much like numerous rivalries in the game, with and without trophies.
Additionally, I'd like rivals to be less static. For a real example, Boise State-Idaho. It's certainly a rivalry game, but it looks like BSU doesn't want to play Idaho once they go to MWC...so if these teams don't play for the next 30 years, it's not really a rivalry game, is it? Much like Texas A&M was an old SWC rival of Arkansas back in the 80s, but then they quit playing each other through the 90s and 00s. They teams have renewed the rivalry with the "Southwest Classic" in Cowboy Stadium, and now EA lists it as a rivalry (didn't list it as one last year). When it comes to dynasty mode, this should operate much like this over time.
If you play a team regularly and the series remains relatively even, they should be added as a rival. If you stop scheduling a team for an extended period, they should no longer be considered a rival. Perhaps what this really applies to most is conference rivalries. If a team moves to a different conference, they should slowly develop rivalries with teams in that new conference, while their rivalries from the old conference should slowly disappear (unless they continue to play each other).
Any rivalry with a trophy should never cease being a rivalry game.