I pretty much agree with NoGlassNoClass. The 2 channel heads are a little warmer sounding due to there being not as much presence. It's a subtle issue though.
This is my interpetation of the 3 channel heads:
The cleans are pretty good on them. The pushed modes sounds pretty good as well.
The 2nd channel is supposed to be voiced toward what the older 2 channels were, but it's a tad bit different. It's not quite as smooth, but it gets the job done. The Raw and Vintage modes sound better to me than the channel cloning options on the 2 channel heads.....especially the Vintage mode.
The 3rd channel has a lot more presence and is more in your face than the older 2 channel versions or channel 2 on the three channel heads. I was able to get some cool Classic Rock tones in the Raw mode with some whacky EQ settings (don't ask me what they were because I've completley forgotten them). The Vintage mode sounds pretty good on this channel as well and the Modern is no holds barred Modern Recto.
There is a little bit more saturation to the preamp gain structure on the 3 channel heads due to the added presence and voicing of the preamp and power amp.
I have an early 90's 2 channel Triple Rectifier and have owned every incarnation of the Recto. I wouldn't discredit the 3 channel heads for anything. They have their attributes and do certain things better than the older 2 channel heads and it's vice/versa. It all depends on your preference and what vibe of the Recto that you want to go after.
The main overall factor is that they're all Rectos. They're just different shades of the color. I like the 3 channel heads as well.
Dale