I have been examining the game and the database for some years, and note that there are a lot of very ambitious user-created league files, including several I have planned for next season. My main one is based in England, so a lot of this will be centred on that. Having not been a regular in this forum, I'm not sure which of these have already been suggested, but there are a few things that in my opinion could be considered:
Club ownership: transfer policy and restrictions, discipline policies
The English non-league scene includes a number of unconventional club structures, for example: university clubs (Exeter University, Loughborough University, UEA, formerly Team Bath), diaspora clubs (as mentioned elsewhere in this forum, based around specific communities), social club teams of various organisations, even a prison team in Division Two of the Staffordshire Senior League. To simulate these situations more realistically, the ability to add restrictions or conditions to clubs would be incredibly helpful:
University clubs often rely heavily (sometimes exclusively) on the student population for their players.
FC Romania were mentioned in another thread recently, but there are many clubs created by ethnic or religious communities (Sporting Khalsa, London APSA, Sporting Bengal United, FC GNG, London Lions to name a few) and it's a shame to either ignore them or let them be just another ordinary club.
British Airways' team is for BA employees and family, so their player pool is very restricted.
Featherstone play (almost) all their games at home, because Featherstone is a closed prison (Cat C). They also have (or had in the past) a policy whereby any player who gets sent off is banned from the team for the rest of the season. For obvious reasons, it also wouldn't make sense for them to sign players from other clubs, sell them, pay them, etc.
Multiple pitches and ground style
With some England mods going as far down the pyramid as they can, many of the clubs included are those that play on public spaces; very few pitches at step 7 or below are actually enclosed grounds. In addition, the option for multiple pitches at one location would be useful for training grounds used as reserve/youth team pitches or public recreation spaces with two or three pitches in use simultaneously.
Isle of Man, Jersey, Guernsey added as nations
Players from these three are currently eligible to represent any UK country at international level. Currently they are included in the database as English cities. Adding them as nations in their own right would lend itself to better accuracy and allow more flexibility. Jersey have attempted to join UEFA in the past, and may try again in future, and there is also a small movement to get Isle of Man in, so the evolution of longer games could include these situations.
Club death, future clubs
Clubs are dissolved and new clubs are created every year. For the aforementioned large mods it would be very useful to at least have the option to simulate this. Similar to the 'New club' field for clubs that are already extinct, it could simply be name and kit options for potential phoenix clubs to replace those that fold during your game, or as protest clubs that might be set up by disgruntled fans. Alternatively, the option to set an entirely new club to create at some point (random or specified year) in the future independent of the fate of others would also serve towards keeping the game fresh and real.
Counties and smarter regional league boundaries
The N/E/S/W boundaries work well up to a point, but have the potential to go wrong. I've found myself creating overlapping areas to avoid unexpected issues. I've often considered that a more effective method might be to create central cities for leagues at lower levels (in other words, the league would be populated with the available clubs closest to a specific city - eg the Anglian Combination's area is a 50-mile radius from Norwich) or to add counties to the database (ie, if a mod creator wants to specify a league to include clubs from Derbyshire and Notts, they could add them to an allowed counties list for that league). This would save the very long-winded method of setting regional leagues for every level for every created team, and would also help for those going to the trouble of creating county cups.
Non-contract players may be registered for two clubs in different leagues (see Jamie Forrester earlier this season for example).
There are a few others but these are the things that are at the front of my mind at the moment. Constructive feedback appreciated.