If I could pick some leagues it would be:
1) English Conference- Finally finish off England, with a proper FA Cup and relegation out of the football league.
2) German 3rd Liga- Add to the German leagues with a strong third tier, making the whole career mode more interesting
3) Brazilian Serie A- Awful it was lost in the first place
4) Ukrainian Premier- Probably the strongest European league without whole representation in the game, would be nice to see this change
5) Greek Premier- Another strong league not fully represented
6) Romanian Premier- Another strong league- would love to play as Steaua Bucharest or whatever they're now called
7) Dutch 2nd Division- Relegation in the Netherlands would make a more intriguing career mode again
Czech Premier- Bring it back, shouldn't have gone in the first place
9) Japanese J-League- If only they could get the league off Konami.
10) Portuguese 2nd Division- Relegation again would make the league more interesting.
One more thing that needs to happen is more Global representation in the ROW, for instance Dinamo Zagreb, APOEL, Maccabi Haifa, BATE Borisov etc
Career mode is a joke when you look at NBA 2K franchise. All you do is play...sim to next match...play and that's it. Why not add things to do during the week like a detailed press conference before/after games where what you say can have impact on everyone such as; fans, players and the boardroom?
Introduce a new training mode and set which days you want to do with Fifa 16 coins pc. Have your whole squad involved in a practice match or get some to run laps to get fitness up and the same time others can be doing free-kicks so you'll have everyone doing certain things to better your squad.
And clubs like Newton Aycliffe, Lye Town, Ely City and Brockenhurst aren't really in demand for FIFA games. But i think having some form of non-league representation on the game even if it is just step 1 (step 2 would be amazing too) would add to the game (relegation from the football league, cup shocks etc.).