They changed the preamp in a big way. But they also tried to maintain the two channels signal path. The cathodes of the lead channels have a 100ohm resistor after a capacitor. The reason for that I believe is because even when activated, the ldr's of the two channel still have a resistance of 100-200ohms. No other hi-gain amp has a resistor in that postion. The two channel has it there to assist in switching from hi-gain to clean. The three channel has no reason for it to be there other than to match the ldr's open resistance in the two channel amp.
I'm not a two channel purest. They have some things that I like about them, and some things I don't like. I have a three channel rectifier and a triaxis. Those two give me all that I need right now. I know someone who swears by his crate blue voodoo. I think it sounds like crap. Some people think the three channel rectifiers are junk, some don't. The way I look at it is if the three channel rectifiers were useless, they wouldn't be selling them. They'd go back to something closer to the two channel amps. The three channel amps are doing it for the majority of the people out there. They are more versatile, have the solo function, and a better clean.
Now there is one way the three channel is devinitivly better than the two channel. Quality control. Ninty percent of the three channels parts are all on the pcb. The two channel has parts on tube sockets, parts on turrets, wires between the output tubes, it's a mess. When assembling the amp the three channel has way fewer spots that a mistake can be made. In mesa/boogies case, this is a big bonus.
Bottom like is which one do you prefer, the ps3, the 360, or the wii. Because the same type of person who argues all day long about which one is better, would probably argue about which of those two amps is better. And it all comes down to opinion.