Your Pioneer is not the only that has skimpy wires inside, My PA-7 and Acurus are the same, I went in and double up the speaker output wires and the return wires. I won't worry too much about the power lines, but yes, beef up the speaker wires. I am not saying it will improve the sound, BUT I can tell you when I do FFT test to look at THD, that extra wire does help......at least on the graph.
Usually the single most import piece that define the sound of the system is the speaker. I don't have enough experience in audiophile to say whether the amp and preamp make that big a difference, I can only talk about I experience from my tests. I tried very hard to make it easy to switch back and fore, I spent days building those fixtures so I can switch back and fore by a switch, no disconnect and connect wires. I don't trust memory, from my experience of guessing wrong so many times which power amp it was, I would not go by memory how the sound is in the comparison if it is close..............BUT, I have no problem telling between my 3 pair of speakers. It is so distinct that no fancy switching is needed. Changing the speaker change the sound completely.
Only other time lately I can hear the obvious difference is when I change to the new speaker cable I made. But I assume you know a lot more about speaker cable than me.
Also, people have different ears, I never ever complain the system doesn't have enough highs, they always sound too bright, I always look for warmer sound, go figure. From my limited experience, you should stay away from tube amps and preamp. You should stay away from amp with JFET or MOSFET particular the input stage. All the opamp I tried that are warmer ( to my liking ) are JFET input stage( OPA2604, OPA2134). Again, don't ask me why as all of them are supposed to be so low distortion that they should not color the sound in any way.......but it does.
Sorry I cannot offer any more. The strongest point I have is the speaker cable which you know more than me. Only thing I can say is whatever cable you use, try parallel one or two more cables and see whether you can hear any difference. Call me crazy, I use 4 pairs for each speaker, I swear I can hear the difference. I use two for the mid/tweeter and two for the woofers. You make cables, so it won't cost you much to try. If it does not improve, you can laugh at me. I swear by this.
I hope you can share your opinion in my thread on speaker cable and THD. There is nothing opinion in that thread, it's all about measuring THD with instrument and look at different cables, experiment with the construction of cable to achieve lowest THD on the load. Only subjective comment from me was towards the end of the thread, I replace the two pairs of 12 gauge Monster cables to the Mid/tweeter connection with my self made cable and found that it has so much more attack, in your face and brighter. I was actually surprised. I was expecting that I won't hear a damn of a difference, that all the measurement, improvement are just like the power amp that is only an academic exercise.
Considering how much measuring etc you've been doing, I doubt I know more than you, more likely just a different school of knowledge or different way of working - what's sad is that I can barely even afford my own cables (the good ones). I primarily make headphone cables, but on occasion speaker related things, and I generally only work with the absolute best wire I can get my hands on, which costs about 10$ per foot of 26awg strands; for speakers that would need to be doubled up ideally to 8 strands per channel for speakers as big as these (ideally even more), and I need 2x2.5 meters or so - some quick math and thats 4800$ just in materials for the wire... To be fair, on paper at least, that would be the best speaker cable it is currently possible to make with our technology (best conducting etc), but I'm never spending that much on a speaker cable - not even half! I have a cable of that type for my HD800 headphone, and thats enough for me

But the point is, I'm an idealist, and thats not cheap in the world of hifi, even the cheapest wire I use would be 700$ or so for a pair of speaker cables-worth of just the wire - I've long wanted to make some cables of that quality, but alas, I have to stick to the "dirty" oxygen free wires like everyone else for my speaker cables, and leave the better stuff for interconnects, headphone cables and rich people... But I still have some pride, so I stick to 11gauge silver plated cables, doubled up as biwire, just to have options, making it effectively 8gauge, taking the resistance in ohm/meter down to around 0.001ohm, and getting lower than that starts to quickly get either very expensive due to quality of the wire as mentioned above, or very difficult, because very few terminals will take wire thicker than 8 gauge - and it would be pointless anyway since the connectors and internal wiring would at that point become the bottle-neck at that point.
But coming back to amps, I've experimented far more with headphones than speakers, and as far as headphone amps, I for years dismissed their affect on the sound, beyond much more than the power needed on paper, and stuck to my portable amp, which was already overpowered. But then I head a Cavalli amplifier, with my HD800, and things changed! I noticed how soft and sluggish my small battery powered amp sounded in comparison! I was morified! So power was definitely important! So I started trying out more desktop amps again, and found that most sounded the same, and didn't have much to offer, but some had a bit of variance; the cavalli, which I dream of (but is impossible to get) has a warm, slightly bassy tone to it, which goes very well with my HD800, where as my Questyle CMA800R has a somewhat analytical signature, and then there is everything in between. Keep in mind though, that headphone amps for all intents and purposes are essentially integrated amps.. Or in somecases they can be used as pre-amps for speaker amps.
What set me on to looking for a new speaker amp, was the massive difference between the massive 20-something kg Pioneer C/M90 which I've been using for 5 years, and thought were fantastic, and the new little 12kg Thule. But it might turn out that even though many like it, for my tastes, the Pioneer is just rubbish, and the thule could risk representing what 99% of other good modern amps sound like, making an upgrade almost pointless... But its impossible to know really, without trying - but I'd need a home demo for that, which is pretty hard to get here.