Great work overall Cubby and everyone else
A few quick issues with the Red Sox...
Kevin Youkilis: is currently hitting .330, but in the game his AVG projects to be .259. I don't know if he'll maintain .330 (he's done a pretty good job so far

) but .259 seems way too low. It also has him striking out 108 times. He's been taking less pitches this year, which (so far) has severely limited his strikeouts. He's on pace to have about 80. Everything else seems fine. He should also be listed as a 1B, as this is his primary position, and he should have the full 200 exp there.
Mike Lowell: The game projects him to hit .261 with 16 home runs. So far this season he's already hit 12 homers, and is hitting .293 (which is down from about .330 after a recent slump. Everything else seems right on the mark.
Julio Lugo: He's hitting .190 with 8 home runs. The game projects him to hit .271 with 9 home runs on the season. So far this year he's shown better power than his ratings would allow for, but his AVG is waaay down. Now, i wouldn't want Julio being released by the AI three days into the season, but he's really been a complete bust for the Sox this year.
Alex Cora: He's been pretty good off the bench for the Sox, hitting .283. The game projects him to hit .246, which is a little low. His ratings need to be raised enough so that the AI sees him as a bench player, not a minor leaguer. He should also be on the major league roster.
Jon Lester: Besides his injury (which has not yet been added) Lester is major league ready whenever the Sox need him.
Josh Beckett: Beckett is on pace for a 3.01 ERA and about 160 ks and is having a Cy Young season to this point. The game projects a 4.19 ERA and only 112 strikeouts. Home runs allowed is also way down, him only having 5 on the season to this point.
Daisuke Matsuzaka: Daisuke already has 110 ks on the season, while the game projects him to have 121 all year. Stuff needs a huge boost. On the flip side, he's already walked as many people as the game projects in a full season (36 to the game's 38), and his ERA is higher than projected.
Craig Breslow: Though he's had considerable success at Pawtucket this year and is probably ready for the majors, I don't think he should be rated to make the team right off the bat.
Bryce Cox: This guy has split time between AA and A this year, and he struggled pretty bad in AA Portland. However you have him with current ratings good enough to be in the majors now at 57/80. The kids just a year out of college and SoxProspects.com lists his ETA as 2009.
Tim Wakefield: He has more Ks than your ratings give him credit for, but other than that not bad.
Sammy Sosa: Ok, sure he's not a Red Sox, but he's not retired either. Of course I'd retire too if I had 1's and 0's in every category except contact.
40-Man Roster: The 40-man roster seemed fine in the last release, but now its all over the place. The biggest problem is the absences of Brendan Donnelly, Alex Cora, and Jacoby Ellsbury.
Also, the Hall of Fame is not complete, but I'm sure you know that.
Good work on the set guys!
EDIT: Is there any plan to add Japanese, indy, winter leagues, college etc?