Trade Logic: I'm a guy who likes to take over cellar dwellers and build them from the ground up (used to do this with my Cubbies, but now I don't have to do that anymore haha). This mainly requires selling off veteran players to get prospects. However, I'm finding that its still very easy (though some adjustments have been made) to steal some top prospects from teams. Often, some of these teams aren't even contenders, they're crappy teams like mine who will trade a young up and comer for my 35 year old reliever in the last year of a deal even though they aren't in contention. Teams need to be more clearly identified as buyers/sellers and should stick to those plans. Sellers shouldn't want aging veterans, and buyers shouldn't want to sell off their MLB talent for prospects unless it fills a certain need. Also, I am noticing that a lot of "rebuilding" teams don't do enough at the deadline to improve. Finally, ratings play a little too much of a role in offers still. High OVR guys with horrible stats costs more than they should, while lower OVR guys with great stats have almost no value. Put more value into stats.
Injury logic: Everyone hates injuries, yet their a huge part of baseball. I turn my injury slider up a bit so I can get a more realistic feeling, however, there's some issues. I see way too many "head fractures" and definitely too many broken bones on pitchers. I don't see enough "shoulder fatigue" or "oblique strains" especially for pitchers. Try to incorporate some more logic into the injuries guys can get. Also, maybe add in rehab assignments and injury recovery setbacks. Finally, serious injuries occurring late in seasons should carry over until next season.
Retirement logic: Speaking of injuries, wayyyyyyyy too many guys retiring with injuries. Here's a list of guys I've seen retire because of injuries: Bryce Harper (a couple games ago), Corey Seager, Julio Urias, and many more young MLB players or high potential, young minor leaguers. In addition, I'm seeing a few too many players retire around age 35 just because their contracts are up, even though they still have been playing well and their OVR are solid.
Contract logic: Going back to wanting to build from the ground up, I'm finding it way too easy to sign free agents. Most of the time, if you just offer the most money you can get a guy. If that doesn't work, just sign a couple of "A" coaches and you're solid. Guys should want to sign for a little less money to play for contenders, because that's usually what happens. Every now and then a guy signs just for the money and that's fine (I'll get into that in a second). Another issue I'm seeing is way too often I'm seeing massive superstars hit the free agent market. Manny Machado, Bryce Harper, Jose Fernandez, etc. all hit the market because teams don't resign them. Guys like this, loyalty usually pays. I'm also seeing teams let guys go because they can't afford them even though they really need them. Example being Wilson Ramos and the Nationals. They have no catchers behind him and desperately need offense. Organizations will clear cap space to sign a guy like that by trading off players (often for pretty one-sided deals, but that's what you do). Finally, too often teams sign a player that makes no logical sense. I've seen the Cubs sign Edwin Encarnacion (even though they have Rizzo) and Wilson Ramos (even though they have Contreras). That can't be happening. Also, guys like that shouldn't want to go there. That leads into my next point.
Player motivations: Anyone who has ever played NBA2K knows this one. Each player should have motivations. Money, long term security, playing for a winner, loyalty to team, location, compatriots, coaching staff, playing role/time, etc. Some of these have been instituted as you can see, but it mainly pertains just to player happiness. I think it needs to be expanded and definitely play a bigger role in contract negotiations. Also, motivations should lead to some kind of contract thought. Will a guy likely resign or does he want out or does he want to test the market following arbitration.
Single A teams: I understand this is probably an issue and makes life difficult for the devs. But I thought I'd throw it out there. There are some players that aren't quite ready for AA, but I'd like to see play to get some extra development
International free agents: This has become a big part of baseball lately. I'd like to see it be added and teams having bonus pool money to spend on these players. You could even hide the ratings and just have a scouting scale to add a little intrigue
Trading: Not mentioned earlier because this is slightly different. Let's get 3 team deals in this game and please for the love of all things holy let me trade more than 3 players at a time (also maybe be allowed to trade international bonus pool money)
Now that's some of the over-arching things to focus on. Let's get into the nitty-gritty things that hardcore baseball (and The Show) fans like myself would really love:
Rotations and Bullpens: I'd like to see an option to have a 6 man rotation. Some teams have started doing this in the second half to save their pitchers arms for the playoffs or keep young guys from burning out too early in their careers. Also allow for a spot start option while simming and be able to identify where in the rotation you want to have your next starter come from (this helps in the playoffs). For the bullpen, be able to identify the types of roles you want guys to have. Sometimes I want to have more MRP and no LRP. Also let me identify SU properly. Like for the Cubs: Stop 7th, Rondon 8th, Chapman the CP. Closer by committee is another thing to consider. Also, CP that struggle should get bounced from their role. I see a few too many closers with 6+ ERAs that are still in their role.
Playing time: This is a big one especially for guys like me who like to use the Cubs and have a super utility guy like Javier Baez. I want his bat in the lineup, but there's no space with just the 4 regular lineups. Let me be able to specify I want him to start in 60-70% of games (such and such at this position, such and such there) and let the simming take care of the rest. I know this creates issues with the lineup, but also be able to specify where guys can hit in the order (like I want Kris Bryant and Anthony Rizzo hitting only 2-4, but a guy like Jason Heyward only hitting 6-8). This might take some toying, but its a huge thing to hardcore players. Also, having catchers specific to certain pitcher (like David Ross for Jon Lester). Identifying player roles isn't a bad idea either, like some guys are on the roster are PH specialists and spot starters.
Season fatigue: This goes is pretty well established, but adding in how many innings a guy has pitched (for pitchers) or games a guy has played (for relievers and position players) compounds over a season in reality, and should in the game as well.
Expansion team option: Like I said before, I love building from the ground up. What better way to do than to literally start with nothing. Be able to pick your city, choose from a lot of unprotected players, etc.
Rain-outs and double headers: This is a part of baseball. Who doesn't like playing 2 for the price of 1? Also, for double headers, allow for a 26th man on the roster for the day like the MLB does.
Being able to identify key players in your organization: Identifying key players in your organization will give them more focus. This leads to better progression for that player over others and makes sure that player gets in the lineup more often than others, etc. Limit it to a couple players, and they lose the ability to be designated as that after they lose rookie status. This also works for the computer teams making sure their core prospects don't get dealt unless absolutely necessary.
Waivers: Actually have teams make you pay for putting guys on waivers. Like if I send a 30 yr old LH RP through waivers at 72 OVR, someone should scoop him up. Makes you be more vigilant to your roster moves