This topic has come up a few times, but put simply, no. Media center will not do this at this point. Although it is my understanding that MC will look at last played info in the iPod (correct me if I'm wrong), the lastfm plugin doesn't pay any attention to this.
The iPod does keep track of your listening and here is the utility I use to submit my listening from the iPod to lastfm:
http://www.lastpod.org/It's quite a pain to do, though. You have to make sure MC (and iTunes, if you use it at all) are both closed when you connect your iPod, otherwise they will erase your play counts from the iPod. Once connected, you open LastPod and it reads in all of the play counts and handles submitting them to lastfm. Once it is complete, you are free to open MC and have it wipe your play counts out (which you would want to do anyway, since you've already submitted them to lastfm).
Because of this tedious workaround, I only do this when I've done some pretty major playing on the iPod... like a vacation or something. I wish this would have got addressed in MC 12, but oh well.