I have played since 2008. The major changes I have seen center around pitching. When I started 2006-2007 pitchers were all mispriced low. When that bug was fixed, the best pitching bargains became the good-hitters like Caruthers and Ruth. As of October 2010 that was fixed and people are using dead ball bagains like Joss, Steele and Nehf.
The other big change I have seen is defense. The sim has gotten better at pricing guys like '92 Daly and '93 Phillips who were out-of-position bargains before. Normalized fielding has made old-time fielders much more useful.