Well, the 'Boogie Archives' (RIP) covered the differences between different versions of the rectifiers very well. The Early Duals, or rev C - D are the earliest iteration of the Dual Rectifier series and sound very close to the Soldano SLO, the amp that inspired them. These are basically uber heavy shredder amps of hotrodded Marshall JCM800 pedigree. (Mark series amps are hotrodded fender pedigree) The gain tone on these amps is tight, articulate, and heavy; and the clean really REALLY sucks.
The Rev E and F are darker sounding and looser. Biggest difference between the E and F is the massively improved clean tone on the F. Most early duals come with the Mark III Schumacher (sp?) transformer while the Rev G (Garden variety) duals have an output transformer exclusive to these amps. I say MOST Rev F duals have the Mark III OT because mine is a Rev F and has the same output tranny as a G.
The big difference with the 2 channel amps is channel cloning. There is an orange channel and a red channel on the two channel amp. When the orange channel is set to variable high gain and channel cloning is positioned in the middle, the Red channel runs on 'modern high gain' mode and the Orange channel runs in 'vintage high gain mode'. With channel cloning, you can have the red channel run in vintage high gain mode, the orange channel in modern high gain mode, or both channels in either vintage high gain mode or modern high gain mode. Orange channel on the two channel duals also dubs as a clean channel which leaves only the red channel to do vintage or modern gain tones. This is how I typically run my head.
Basically, the RED channel on Revision F and G 'garden variety' 2 channel amps are fairly close to channel two of the three channel dual. The biggest difference is really that the two channel seems to have more bass and more organic / sweeter of a tone. Still, if you set up the dials correctly, you can get settings that approximate what can be achieved on Channel III of the modern dual, provided the tones aren't *too* extreme.
The ORANGE channel is where the true difference lies:
1) The clean tone. When channel 1 is set to clean, there is this buttery warmth that the three channel amps don't have. It is subtle, but an improvement nonetheless. I find that with high quality EL-34s, the clean is comparable to most good tube amps at least on my Rev F. When the bass is set too high, tube breakup can get flubby which is really not a nice effect, but with more reasonable settings you can get anywhere from a squeaky clean to a nice blues overdrive.
2) Variable high gain. This is where the two channels really shine. That same added warmth that is present in the clean settings on the orange channel also makes for a fairly serviceable lead tone. On the red channel, dialing in a good crunch for chording is easy but single note work-and especially leads-really suffer. They feel brittle, thin, and generally quite stiff in nature. When gain saturation is added, they are better but still only acceptable. Generally, they are very close to what you find on the three channel head. On the orange channel, when I refer to a 'serviceable lead tone', I am talking in comparison to an amp known for good lead tones. When we were doing test run #2 with my buddy's 3 channel and my rev F, I decided-for the first time-to try my orange channel in variable high gain mode as a lead channel. I was suitably impressed by it. The lead felt organic, vocal, and very elastic, with tonnes of sustain and a super thick warmth. The notes literally seemed to jump off of the fretboard. I think this was a point of revelation for me. This amp was designed with only a serviceable clean, specifically for use as a distortion amp. The intention really was to use a different head for clean tones. My general impression with my amp is that the orange channel is simply voiced differently and the added mojo infused into that is present no matter what the channel cloning settings are.
So in my opinion, based off our tests, I'd say that the orange channel from the Rev F & G dual Rectifiers doesn't really exist on a three channel Dual. To determine if this is the case with a Roadster / Roadking, tests would have to be done but I'd assume the results would be similar. Perhaps someone who owns a Roadster and a 2 channel dual would care to comment on this . . . The Red channel on a two channel dual is essentially the same as channel 2 on the 3 channel iteration, at least in Vintage and Modern high gain settings. Channel 3 and the clean are both different. When we compared our amps for round #1, we really didn't crank them up at all. When looking at the orange channel on my amp, we assumed it to be 'clean' and my friend simply commented that my clean settings sounded 'good' and he wanted to copy them. That was that. It was only at round #2 when we cranked the amps up and I tried variable high gain mode on my head that we really got an idea of the true difference between these two beasts. Now don't get me wrong, I'm not saying you can't use channel 2 on a 3 channel dual for leads, you can. It does work and good tones exist on that channel for that application. I'm simply saying that the difference with the orange on the two channel dual is quite pronounced, perhaps much moreso than I initially thought. In my opinion, the lead tone on this channel was really good, and that was with the same settings as my rhythm tone on the red channel. I haven't even really tweaked it to optimize it for lead playing yet.
I talked to my wife and I think our long term plan is to get an ABY switch and an Electra Dyne combo. I LOVE the cleans and the gain options on that amp and I think it would replace my Peavey Rage158 very nicely. As for the Dual, at my earliest convenience I intend on running it for the purpose for which it was designed, as a dedicated distortion amplifier. As for now, I'll just run the gain higher on my Red channel and use the volume knob on my guitar to switch from rhythm to lead. It seems like a great stopgap solution until we finally have the $$$s saved up to run a dual amp setup.
Anyway, sorry for the TL;DR essay. I always assumed all the recto amps to be pretty similar so when we actually tested things, the results were rather surprising. (The most resounding point of agreement between my friend and I was that both heads sound better with high quality EL-34 tubes) Both amps do sound great and people who buy 3 channel duals aren't making a poor decision. The reality of the situation is that they are both different amps with unique positive and negative points. (the 2 channel Dual would be greatly improved with the addition of a stellar dedicated clean channel, for instance) It is up to the player to decide which amp is the best for what is needed at any given time. That being said, I'd like to encourage those here who own 2 channel duals and have not run the orange as a lead channel, try it. See what you think. I'm curious.