I have my doubts about how much of his problems were injury related. For those with a BP subscription and for those without:

Take a look at the spread of flyballs, doubles, and home runs in 2005—Bay is all over the outfield, but his pull power is the highlight of his hitting prowess. In 2006 we still see homers to left, but they travel a bit less while his doubles there decrease. For the 2007 season, his production to left has all but disappeared. However, note that this is just the data from his home park; his directional charts, which encompass all of his batted balls, tell the same story...The largest portion of Bay’s balls in play are grounders to the left side of the diamond, and although he is collecting a solid number of infield hits, Bay is around so that he can slam balls over the outfielders’ heads. The issue of course is that Bay’s pull power isn’t as present as it has been in the past, with Bay often grounding out to the left instead. The fact that he’s going the other way as often as he is without pulling the ball successfully makes me wonder if he can’t get the bat around fast enough on inside pitches, and has to make outside pitches that go the other way a more significant part of his game...Unless it’s down the middle, Bay can’t do much with it when it’s inside. He’s still hitting the ball in the center and outside parts of the plate though, which you can see reflected in the directional chart and hit charts above...Bay's pull power is what made him such a great run producer; without that, he’s just like those players he has been compared to throughout his career.