I'll reiterate quickly some of the ideas that have already been mentioned:
- Definitely more logo slots. Four would probably be fine.
- Separate slots or some other feature to add manufacturer logos (adidas, Russell, Nike, etc)
- Ability to resize and move the logo on the helmet.
- Uniform updater. I don't think any schools uniforms stay exactly the same for more than a few years at a time, some change yearly (unless you're Penn State). Have this option for TB teams and real ones.
- Pride stickers, including ability to slot in a custom-designed sticker.
- More equipment options.
- More sock and shoe styles.
- More styles (templates) for helmets, jerseys, pants.
- Extend chest text character limit. 10 characters is too small. Also have ability to wrap text around the number (top & bottom).
Now some that haven't been mentioned:
1. Custom Font Uploads/More Fonts - This refers to the ability to customize the font used on your team's jersey by uploading a font from your computer. If not feasible, at least include more font styles than three for names, numbers, and chest text.
2. Layering styles - Using a "layer" system (such as the one in NFSU) to create more dramatic styles as well as combine different templates. As an example, each jersey would have three or four usable layers and each layer could use a different jersey style with different colors.
3. More extensive customization - Perhaps use more Photoshop or similar graphical program integration so that users can fully customize the field art or even create their own jersey templates.
4. Fix bugs - An example would be the weird looking font text in-game (looks very pixelated), and the grayed-out stadiums. Also colors going dull at night needs to be fixed (namely the white helmets), but this is more like a gfx issue and not TB-related.
5. Dynamic uniforms - This includes conference patches and so forth that can change over the course of a dynasty. Perhaps your school signed a new sponsor deal as well with Nike instead of adidas, so those logos would change.
6. Other details - Different font effects (such as shadow); placement of details on helmets (like jersey number); and other small things that you will notice on jerseys but are not editable in TB currently.