A little less than a year ago, I was similarly debating a change to either Boston Acoustics VR3s or Axiom M60 mains. While I did not have the opportunity to listen to the M60s, I had previously listened to the VR3s and was quite pleased w/their performance. Having found a very good deal on the VR3s, I opted w/the BAs and haven't been disappointed in the least. The VR3s sounded a bit better to my ears in comparision to the VRM80s, but the 90s are impressive, just a bit out of my price range.
I actually have a pair of Axiom QS8 surrounds and M3s for rear surrounds and I'm quite pleased with them as well. I've given the M3s a good workout as mains just out of curiosity when I purchased them and they're very good performing bookshelfs, well built also.
I really don't think you can go wrong with the VRM90s/VR3s from BA or the M60s from Axiom, both would give you some solid mains as a foundation to build upon. The VR80s aren't quite worth the money (IMO) over the VR3s and the M80s are very similar to the M60s, just a bit lower in extension and can handle more power, but if you plan to use a sub with these, chances are it wouldn't be necessary. Plus, the M80s are 4 Ohm as opposed to the M60s 8 Ohms. The VRM90s are the better looking than both the VR3s and M60s w/the real wood veneer if that's a consideration.
One other thing to mention, AudioAdvisor is having a heck of a deal on the BA VR-M series right now. The M90s, VRMX surrounds and the VRMC center (which I'm not terribly fond of) can all be had for a good discount, they're all also offered as a package... -TD