I suspect most of these would be rather small changes and many of these come from the additional perspective of an online league commissioner.
-be able to select a league from the opening screen instead of loading the current league and then having to go through the menus to open a different league
-being able to release, trade, demote, promote, extend, disable list, 40 man a player from anywhere in the game by way of a right click menu whereas a left click opens the player screen
-not be able to move a player to the DFA area and waiver area, only way you can have them do that is as a consequence of removing them from the 40 man area, the active roster, or as an option after moving them to the trade block for the purposes of: dumping salary, judging trade interest, to trade after the trading deadline, to decoy for trades.
-options to backup up only txt and dat files, or boxes and logs, or both, but never p*.html as they're regenerated whenever you want them anyways
-during the playoffs have links in the league menu to see the standings screen and playoffs screen. normally you only see the playoffs screen and if you want to see the year end standings you have to generate the standings report.
-have links in the league menu to see the rule 5 draft and spring training screens instead of having to wait until FA and the ammy draft are done
-have links in the team menu to generate the salary, current/recent financial, and financial history reports instead of having to go through the front office screen first
-include ability ratings development to the dev reports
-list DFA'd and waived players on the team report like say under the DL
-increase the top prospects to the top 20 (please? and maybe increase the league wide one to top 200 too)
-separate the transactions report into releases, waivers, trades, DL, promotions/demotions, FA signings, extensions, etc reports
-track all changes in financial factors (e.g. market size, fan loyalty, fan interest, ticket price, etc) and figures (cash, the different revenues, expenses, attendance, payroll, cash, profit, etc) rather just what is in the financial history report and more like how the dev report does it so you can see exactly when in the season something like fan loyalty changed and noting everything for the season start and finish
-have financial projections like what should revenues, expenses, profits, budgets ($ left for...) be at the end of the season, beginning of next season, and maybe even at the end of every month of the current season
-fix the $ left for extensions formula to = (Last Year Merchandising Revenue + Last Year Attendance Revenue + This Year Broadcasting Revenue + Cash)
- (This Year Salary of Players with 2 or more years left on their contract + Next Year Salary of Extensions + This Year Salary of Coaches +
Arbitration Estimates) instead of what appears to be approximately 94% of Arbitration Estimates. That is, in the budget formula you seem to use a value for arbitration eligible players that is not the estimate nor what they eventually get, but for most players it is about 94% of the estimate for some strange reason. And get someone to correct the FAQ about this.
-if a player cannot be awarded arbitration less than his current salary then never give an estimate that is lower
-better organize the league files (in the league folder, not the generated reports folder) like how all p*.txt files are in the players folder, put all boxes in a boxes folder, logs in a logs folder, misc in a misc folder, etc instead of throwing most everything in the league_news_bx folder. It would make it a lot quicker when looking for a file.
-fix the box scores so the logos show up
-have an actual league wide trading block screen, instead of just the report, with a link in the league menu
-put a link to the league wide player list screen in the league menu, instead of having to get to it from the almanac screen
-have an actual league wide possible FAs next year screen, instead of just the report, with a link in the league menu
-generate amateurs a year ahead of time and have a screen to them so we can dream of getting to draft them for the entire year like we do in real life
-keep more records
-have more leaderboards
-associate name files (some of us use different name files for different leagues) and default player photo (some of us like to use a league's logo there instead and if you ave more than one league you can't) with a particular league instead of having the same for all leagues
-give us more name file options like the originator mod does, which appears to be pretty popular
-add in fields to the manager screen to input your email address, AIM, MSN, and yahoo IDs that other online league managers can click on to contact that manager
-be able to choose and remember the styles.css file you want to use when generating reports for that particular league instead of having to change it every time from the default
-clear all rookie records button
-fix the records like where the rookie batting average record sometime doesn't pick up
-be able to input league wide financial factors like market size, fan interest, etc and figures like both local and national tv deals, etc instead of having to input each and every team's value to the same
-make the minimum cash level inputtable like the cash maximum level is so that teams can't dump high-priced players and not be hurt by it
-do away with the silly revenue sharing system now in place and instead have some better and optional revenue sharing systems
-be able to edit the draft order without having to use a 3rd party editor
-be able to select the all-stars instead of having to use a 3rd party editor
-change the height exporting system to something where you don't have to reformat the csv to d-m before reimporting it
-try and make more quality FAs get signed during the FA period instead of having some leagues having to hold a special FAP to get those quality FAs signed
-show mins, maxes, means, medians, etc for stats and financials
-in the main screen list the win/loss records of all the teams for some inputtable number of games like how many online leagues like to see the record for the last sim instead of the no matter what last 10 games
-in the main screen or another screen list the games back for wild card races, not just the games back for the division race
-in the online league setup screen have a folder for exports and one for reports as some of us like to separate the two
I could come up with many more, but this is on short notice.