The following is one of the most important and fundamental structural changes OOTP could make...
SUGGESTION
Make
ALL leagues truly separate, unique leagues with their own rules, options, league totals, and settings. Leagues could then be grouped in associations (see the
league association proposal). Subleagues would be retained but mainly for recreating conference structures in a league.
REASON
This would allow for maximum fictional flexibility and much better historical authenticity. No longer would one recreate MLB by having the AL and NL as subleagues in an MLB league and thus have to use averaged out league totals or rules as a result. Instead, the user would recreate MLB by creating an AL and an NL, and then making them a part of an association called MLB. Doing it this way allows each league to retain its own individuality in terms of league totals, rules, and so forth, while still operating under a common framework in regards to player movement, drafts, etc. Users can also adjust how each league or association interacts with all the other existing leagues/associations (with the options based upon the interactions which have existed in the real world).
PRIORITY
High.
There are certainly many aspects to this suggestion which would need to be carefully thought out, but I've spent a lot of time thinking about how this could be structured and researching the real-world models. I can present quite a bit more detail if requested.