The 3.1s have a different magnet for the mids, now neodymium, an updated crossover and they have eliminated the tweeter cut/boost switch. I would go with the 3.1s if at all possible, look on Audiogon.com for some great deals on gently used pairs. I purchased mine (3.1s) off Audiogon for a smokin' price, $1700 delivered to my door. They were in perfect condition and, as a bonus, because they were used they had already been broken in. This is VERY important for these speakers, they absolutely sound better after they've been run for a couple hundred hours.
They are, without a doubt, the finest speakers I have ever owned, and I do not foresee "upgrading" them for many, many years. I've mated mine to the Gallo Dues which I'm using for my center and surrounds and the sound is marvelous. I am also using a small Earthquake subwoofer to augment the bottom octave. It took a little while to setup the subwoofer to integrate properly, but now that it's done I'm extremely pleased with the sound.