Giving this topic a little more thought, I'm struggling to come up with a definitive answer, as I'm aware that it's been a really long time since I've heard many of the configurations in question - let alone used them.
Memory is not the most reliable form of evidence, especially given the time between different series, and the time since the brand's ubiquity - there's inevitably a large dose of nostalgia for any given device.
I still own, record, and gig with a mark IV stack (AH250 GP11 amp, 1048 + 1518 cabs).
The mark V supposedly had some improvements to the signal path, and some folk feel the EQ is sweeter, than on the mark IV.
Other than up-rated power,a 12th band of EQ, and latching switches, I don't remember what Series 6 improved upon, over mark V (the overall design aesthetic was an improvement).
I do remember one of the original Trace engineers, saying that the changes to the power section was, in their opinion, the biggest mistake they ever made, in terms of signal integrity - though I can't truly remember if that comment was directed at Series 6, or the SMX range).
SMX introduced bags of features (valve & solid state input section, multi-band compression, tone balance control, Kevlar impregnated speaker cones, HF horns in the 10" driver cabinets, up-rated power handling).
The Gibson era solid state amps added tons of connectivity options, but took an aesthetic nosedive.
The VA, and Duo / Quad / Hexa valve amps, of the mark V, and Series 6 eras, were a brilliant fusion of cutting edge tonal sculpting, combined with everything we love about valve amps - it's just that I was done with valve amps at the time, or I would have shown more interest.
Likewise, with the V-type (V4 / V6 / V8 / Hybrid) range - I was no longer looking for valve tones, and it seemed as if Trace Elliot was deciding it needed to compete directly with Ampeg, which at the time felt like Trace management were overlooking what made them stand out / successful - of course I would later come to appreciate the V-types, in their own right.
And lastly, the recently discontinued big stuff by Peavey - some aesthetic, and tactile misgivings aside ; the only reasons I can think of that these didn't seem to be selling are :
1. The ELF didn't exist yet, so folks who don't want the big stuff (yet), didn't have a route to grown in to the brand.
2. Inadequate marketing, and celebrity endorsements.
So, if I'm forced to pick favourites - based on the sheer number of stages I've seen them on, and records I've heard them on, it would have to be :
Series 6 GP12 / mark V GP11 with 10" Celestion drivers (no HF horn), and 15" Fane drivers.
However, in terms of products I'd like to see available...
Big Stuff
Solid State :
The sound of mark V / Series 6, with the features of SMX, and the drive section of the Peavey era, and possibly the more compact Peavey era cabs, but with a slightly more Series 6 aesthetic.
Valve :
A return of the V-types, with sealed cabinets.
Small Stuff
A more powerful, more fully featured ELF - perhaps 5 band EQ, dedicated control/bypass of compressor/limiter, pre-shape, and DI with pre/post switching.
Studio Stuff
Software :
Free AAX / Audio Units / VST pre-shape plug-in.
Fully modelled mark IV / V / Series 6 / SMX / Peavey / V-type pre-amps.
Fully modelled mark IV / V / Series 6 / SMX / Peavey / Duo / Quad / Hexa / V-type power sections.
Fully modelled Celestion 10" drivers from the mark IV / V / Series 6 / SMX / V-type / Peavey eras.
Fully modelled Celestion 12" drivers from the V-type range.
Fully modelled Fane 15" drivers from the mark IV / V / Series 6 eras.
Fully modelled Celestion 15" drivers from the SMX / Peavey eras.
Including full emulations of the guitar (Tramp etc) range, would broaden the appeal considerably.
Logically, a partnership with IK Multimedia, would take the hassle out of this.
Hardware :
Passive, and Active DI boxes, featuring direct, and switchable Pre-shaped signal.
I think it's going to be hard to glean much more than what was popular / what are people still using / what's still surviving / what did people have ambitions of owning when they became a rock star / what are people nostalgic for.
If Peavey could re-amp a clean bass signal, through a selection of Trace Elliot's amps and cabinets (mark IV / V / Series 6 / SMX / Duo / Quad / Hexa / V-type / Gibson / Peavey), of like vintages, in a controlled environment - and then conduct a poll, where we could put our favourites in order (perhaps isolated, and in a mix), that would be pretty definitive, and useful...
Or alternatively, crack on with IK Multimedia, and use Amplitube as a means of gathering market research, as to what is the most cherished configuration.