What a fascinating thread, sad to be late to the party!
I sort of feel that the argument has been pretty much sewn up - Mills's assertion that editorially mandated ideas made 2000AD bad in the 90s is just not true - or at least, not entirely true. They may have been to blame for him not trying his best to write great stories in that decade.
I'd like to add a couple of comments. Much as I struggled with Mills's Slaine work in the 90s as I read it in the weekly Prog, I really enjoyed reading them in one big go in the reprints. I guess this is a LOT to do with the improvement in printing technology, as I recall Slaine being by far the worst offender for brown-mudness (along with poor Nick Percival's 'Goodnight Kiss' epic) - even Bisley's Horned God suffered a lot. It's also a lot to do with Mills himself apparently thinking more along European album lines and less along weekly episode lines. Compare Book 1 of Nemesis the Warlock, which has a lot of stand alone episodes strung together, with, say, Slaine's 'Demon Killer'. Basically, I found most weekly epsiodes of 90s Slaine and later Finn pretty much incomprehensible. Read i a chunk, and they're really rather good - even the Secret Commonwealth has some fun ideas, just poorly executed.
The other big thing is that my memory of reading comics in the 90s, primarily 2000AD, the Meg and various Marvel comics, is that the art in 2000AD was always the best, and that Tharg always seemed able to find exciting new artists who worked in a wide variety of styles. There were a bunch I hated / thought weren't very good, but it was still exciting to get that shock of the new. And a lot of the ones I didn't like at first were, miraculously, given room to develop into some of the best going (e.g., for me, Simon Davis, Carl Critchlow). Good artists can make a bad story way more palatable - I'm thinking of Kev Hopgood on Dry Run, Dillon/Walker on Harlem Heroes and so on.
I imagine it's nervewracking losing your top creators to other comics, but it's energising, too.
Statisticians may be interested to note that John Wagner has provided far fewer stories for 2000AD in the noughties than he did in the 90s.
The longest stretch without a Wagner story in the Prog was the opening of Judgement Day in Prog 786 (which he co-wrote don't forget) to 'The Time Machine' in Prog 889.
In other words, two years worth of Progs - but, if you were reading the Megazine, you'd get a single or double or even triple-hit of Wagner each month/fortnight during the same period.