But, if you have a choice between two cameras of different formats and different megapickles, go with the bigger format. (With, of course, the usual caveats that sufficient technology age can skew the results.)
Except 1D MK III vs 7D.
Oh wait, the 1D MK III ist two years older, I can't compare them ...
Just joking... as you said, due to technology developments (and other reasons, as discussed) it doesn't make sense to compare sensors only in regard of size. (And likewise the whole thread doesn't make much sense IMO).
Eh, not exactly.
Until relatively recently, comparing formats was commonplace and trivial. The exact same film you loaded in a cartridge into your SLR was being used in large format backs. And you really had to be clueless in those days to insist that you could get the exact same quality out of the smaller format.
We've been in a rapid growth phase in the digital world where, in about a decade, we're seeing quality improvements comparable to what used to only be achieved by going with a larger format. The latest-and-greatest APS-C sensors have basically caught up with the earliest full-frame sensors. Those first full-frame sensors were going toe-to-toe with medium format film; today's full-frame kits outperform the view camera that Ansel Adams used -- and today's high-end medium format kits surpass anything anybody's ever had access to, perhaps with the exception of some of the insane custom setups.
However, there's very good reason to suspect that this age of rapid growth is just a phase, and that it won't be all that long (historically speaking) before it'll come to an end. Eventually, we'll be back to marginal improvements, and all camera sensors will have roughly the same pixel densities and noise characteristics and the like. When that day comes, once again, the defining characteristic will be format size, not sensor technology.
And we even see that to some extent today, within a manufacturer's lineup. Canon's currently-produced full-frame cameras outperform their currently-produced APS-C cameras by about a stop or so (what you'd expect), and the same is true with Nikon's full-frame v
APS-C, and Sony's, and Leica's, and so on. Between manufacturers the lines aren't always so clear...but, then again, there were always wars between Kodak and Fuji films.