I have been playing this game since 1996, and it gets better every year.
Geographic Maps - One improvement I would like to see is more emphasis on the geographical location of clubs. I would love to see a map with the club emblems pinned, ideally with links to that club. This could be achieved by the Geo coordinates that are within the database for each city perhaps. Although this alone would be a cosmetic touch, to make it more functional, the current scouting could also utilize this. If I take control of a club in the conference leagues, I imagine scouting would be limited to my surrounding areas and therefore we could highlight those areas on the map. Another way to make this more functional would be to allow us to see our youth recruitment catchment area?
Leagues - The MLS is currently a very insular league, but every now and then it will add a new franchise to the league, such as the upcoming NYCFC. It could make the longer games more dynamic if league rules could change every now and then to allow this, or at the very least a manual with the advanced data editor so that we can add this in ourselves. I'm no newbie to the editor, but the amount of trial and error testing to get something working can be a bit of a nightmare.
Kits - please allow kits to change every so often. It's weird being 30 seasons in and still using the same kit. I'd love to see a slight variation each / every other year like in real life.
Media - if I have taken a team from the lowest division to the highest, I want that to be commented on in the media. Make it more personal, so that your legacy is defined in the history books, rather than just comments of overachieving. Additionally, if I choose to leave the club, I'd like to have an exit press conference (unless of course I'm fired).