First, foremost, & most important. Thanks to: Cubbyfan23, haveband, Muzamba, injury.log, IcySpanish, Exodor, Underlined.i, rdklein, & everyone Cubby didn't mention. Thanks, that's a lot of hard work and sharing all that work deserves more than a thank you can cover.
As for my analysis, I ran a two year sim, and even added college & high school feeders. I find the set to be solid, but I see why you made a list of issues you already knew about.
1) The financial are solid, just arranged add is all. Second season all was good. Didn't find this to be major.
2) League Totals I found pretty solid too. Averaged out over two years more so. AL Pitchers were fine in my sim. Johan Santana even won the pitching triple crown in the AL.
3) The biggest thing which I found was the ratings of prospects. You were right on that. You may have even understated the issue. (Tim Lincecum 2007 total 300 K's) Tampa Bay has performed way too well in every test sim I've seen and done . Washington won the NL wildcard in my 2007 just beating out the Marlins. This must be a reflection of the prospect ratings. Maybe, this has some impact on my 4th point.
4)I also had a slew of weird releases like the ones you've mentioned. Craig Biggio (didn't get his 3,000 hits), Tim Wakefield, & similar players of high age & experience. I also had guys like Homer Bailey released. All before the season started. I'm wondering if the releases in general don't maybe have something to do with the AI's perception of the odd financial arrangement. Maybe, the release of older, experienced, high salary guys has to do with the very high ratings of prospects in all the teams systems.
Otherwise no crashes, errors, anything else wrong. A solid set. I thought you'd just want to see what type of results other folks are getting. I'm in waiting in one of the leagues planning on using your set, I can see it's going to be worth the wait. Thanks to all again.
PS: No Joke- I have one eye. Maybe that's why I don't see the Pulaski Blue Jays anywhere.