The reason I think a lot of cheap amps get decent OD tone but not good clean tone is because they are relying on tone stack and preamp distortion to get the OD tone, and there's a lot of "shape" in that tone. Not only that, the heavy overdrive masks a lot of detail and dynamics of the guitar that are bare in a clean tone. So in those same amps, that rely on the preamp clipping to make "overdrive" tone, there's really nothing there to give any dimension to the clean tone when you turn the gain down.
So the key to an amp with good clean tone is balance throughout the whole thing, all the way to the speaker.
Most of the crap clean tone I hear from guitar amps is due to no real amp compression happening, poor detail (aka masking the guitar's tone), crummy pickups or a guitar that just sounds bad acoustically, and/or the amp is just not turned up loud enough to make this happen.
So like my Princeton Reverb with the Weber P12R will get the most glorious clean tone on earth when you crank it until it gets some crunch, then turn down the volume knob the smallest amount you can turn it... This really is an overdriven tone but you don't really notice the overdrive. But it's driving the speaker hard enough to get it to compress and the amp is contributing some 2nd order harmonics to the tone to give it some "richness", but the amp is not clipping heavily enough to mask the shimmer and texture of the guitar tone. Put a decent LDC or even my ECM8000 in front of it and you can't miss.
My Classic 30 clean tone was like dog breath with the stock speaker, mostly because the stock speaker didn't really have any decent top end and instead of compressing, when you cranked it enough, it just kind of went "splat". Crank it a little bit too much and it gets buzzy (3rd order distortion). So you are left turning it down too low to get any compression out of the amp, or any harmonic addition at all... way too clean and sounds sort of like the guitar's plugged into a DI with EQ. Put in a speaker that'll take some heat and give you a bit of compression and viola. In my case I wanted a British type of tone from the amp and get it in spades with the Eminence Private Jack.
Crap speaker in the Pro Jr. does that "splat" thing really well, but on top of that, it also has no top end or bottom end. Just a midrangey mess. Same for the AD15VT. It takes a real special 10" speaker to get any useful bottom end, and likewise it takes a special 12" to get shimmery top end.
I second the Weber speakers ... but for half price, don't overlook Eminence. Go hit avatarspeakers.com and order a 2x12 cabinet, put an Eminence American-style alnico speaker in one side, and a Private Jack in the other, wire it in stereo and plug clients' amps into whichever side works for the tune (either you want Plexi, or you want Fender). I bet the fix-it for most tube amps' clean tones is getting a decent speaker in there.