Thanks a lot for the suggestion. Unfortunately, the tagger isn't smart enough to really do that - it mostly just tries to extract the title and search based on that - there's no 'feedback' logic.
Even if it could figure it out, 'Fruits Basket S1' would likely take precedence and hence, the first season (that is, first thing that aired) would be preferred anyway. Using years arbitrarily can be problematic as AniDB often tags sequels and OVAs using it; you could probably build something which introspects all matter of things, including series sequel data, type etc, but, as you might see, it gets complicated if one wants to be careful about it.

There's limitations with how the current auto-tagger works, but trying to rebuild it means re-implementing many rules that the current code has gathered over the years. Maybe I'll attempt it some time.