First, there is too much info on the main page. The old layout was basically one-click to get to the information you needed. Now you need to find it on the left, then at least 1-2 more clicks to get to it.
Second, it looks like you can't look at year-over-year anymore. The old site let you see, for example, the TD leaders for all years on a single page. Is that still there?
Finally, the search function now looks at the ENTIRE name (including middle). I'd prefer the default search not be that detailed, and then have an advanced search if it doesn't turn up.
Aside from navigation, the pages take FOREVER to load.
On the plus, once you actually find the detail page you need, it seems like there is more data. I like the hover-highlight, too. It's a bit cluttered, though - it would help to have vertical delineations between the types of stats. For example, CP's rushing/receiving stats and then also within the defensive stats:
Clinton Portis Statistics - Pro-Football-Reference.com