I like the newer ones better. I thought they sounded warmer and Mark confirmed this. He has warmed up his amps a touch over the years, based on changing tastes and more experience. They are still very clear amps, and definitely not too warm.
Plus, Mark is always learning, testing, experimenting... with the tiniest of details. If you buy the latest, you generally benefit from this. I don't think things have changed dramatically, but he's the kind of guy who might go from 7 screws to 6 on a cabinet, because he hears a sonic improvement. He is definitely dialed in on every part.