I assume you are also an actual OOTP player, but if not, obviously all those concerns are mostly addressed by the full Win/OSX/Linux package.
There are major limitations on the iOS platform when porting a database behemoth such as OOTP over. You are unlikely to ever have a full minor league system/ FA pool (for example) because it would make the app's footprint 3x larger than it already is. All of the other features like waivers, options, MiLFA, and better AI require lines and lines of code as well which degrade performance (remember, iPhone CPUs/RAM are essentially what you had in your high end desktop 10 years ago) and add to bulk. They are no doubt working out a lot of the kinks for next year (this is iOOTP's first year) but iOOTP will still be a 25% version of OOTP for the foreseeable future due to device limitations.
Yep - played OOTP 6 and 10. Would play the PC version if I owned a laptop - I like having the game on hand while watching TV and playing between commercials. I did read somewhere that some of the decisions they made had more to do with targeting a casual audience than the device limitations (the iPad is probably more powerful than the laptop I used to play OOTP 6 on 8 years ago). I did play 68 seasons, so it's not like it was awful, just too easy for me to play endlessly. The big advantage of the easiness is, since there's not a whole lot to do, you really can rip through seasons pretty quickly. One of the reasons I stopped playing OOTP 10 was because I spent so much time working on minor transactions that I never built up enough seasons to care about my team. Picky, I know.
So I guess my main complaint is not with the robustness of the minor leagues, but that there needs to be some more mechanisms that prevent me from assembling ridiculous superteams. You're probably right that it'll come in next year's game.
FWIW, what I do is:
Trade any arb-eligible relievers for prospects immediately following the season.
Sign my own players the year before they become arb-eligible to extensions that expire during the sixth service year.
Sign any players in their sixth service year to four-year extensions (usually <$13M the way the system is set up).
In years where I have low draft picks, draft elite relievers. This has the added effect of making other teams need relief help.
In this system, I'm guaranteed 10 years out of every elite player and retain the flexibility to trade the players if they start losing their skills before the contracts are up or if I can replace them with cheaper talent. If a player is still elite in his last year of the contract I just let him walk for the picks. Eventually, I end up with an elite team of players for somewhere around $120M. Then with the surplus payroll I can either fill any needs I have left over or pick up guys on one-year deals (either through FA or trade) who will yield picks. The talent distribution in the game is such that keeping players on your major league roster for 10 years gives you enough time to incubate their replacements.
Some more pros and cons that I didn't mention earlier:
Pros: Game Center integration, pretty fast sim/save, touch interface (especially for setting lineups).
Cons: Ignores screen switch, text can be too small in some places (iPad version), crashes a lot.
