I think it has to be the speakers. They dictate available choices in amplifiers. One could argue that amplifiers could row the boat, but from a practical standpoint how much sense does it make swapping speakers? They are a royal pain to ship, unpack, pack, ship. Plus, the speaker/room connection cannot be denied and the room ain't going anywhere.
How about trying to voice the rest of the system starting at the source? This is guaranteed to produce frustration, akin to using a rowboat rudder to steer a battleship. You might get there, or you might wind up in Guam.
To some degree, it's a trick question. Any true strength in the system is only that when properly supported. A different supporting team will not show all its wonder. Twenty combinations might be possible which would satisfy the listener but there is no way to audition hundreds of combinations in one's own room to find out.
So, the theoretical question must be converted to a practical solution and that is, if starting from scratch which piece is chosen first? Pragmatically, it has to be the speakers.
As to the thoughts on adjustable crossovers and EQ, I agree with a lot of that. I have been using a TacT to perform these functions for some time and they are incredibly valuable. I used to really get worked up about tweaks and cables and such, but since having the TacT I don't sweat them any more. Now, the TacT isn't perfect and I'm working on coming up with an alternative to compare.
The TacT has enabled me to play with all manners of crossovers between my main speakers and subwoofers. I have found in my room that crossing over at 65 - 70 hz creates an ideal blend. The subwoofers will end up with Zu's solution of a parametric EQ while the mains will (for now) use a Harrison Labs Fmod at 70 hz and 12 db/octave. I've used these gizmos in the past for low-pass to subwoofers but I've never tried them for mains duty. They're RCA in/out, line-level crossovers that run about $40 delivered.
This solution won't, by itself provide anywhere near the flexibility of the WLM or TacT solutions. It will allow correction in the bass area, which I think is most important. It will require a leap of faith that the rest of the spectrum is balanced. If one is into computer audio, there are other choices to fix the rest but they're fairly involved and not for everyone.
The audio purist would point to WLMs solution and cry "loss of transparency!" Having not heard them, I couldn't say. That WAS the reason all those handy controls disappeared. I have a sneaking suspicion that if those controls came back, cable designers and tweak merchants would be mighty worried.