I'm not entirely sure if it was a transformation of the industry as much as it was a transformation of the marketplace - on this I agree with you 100%. I think the industry lagged behind until mid-2001 - there's a long period of just drek where sales were in the toilet from the late 1990s. Amazing having a print run of under 20,000, things like that.
Yeah, I agree with that distinction. Consumers reacting instantly, while publishers and retailers were a lot slower on the uptake.
I would put the "Modern Age" starting with Amazing Spider-Man 30, Fantastic Four 60, some of the other reboots that started right around then. Maybe Daredevil 1? There's a completely different feel from Amazing 25 to Amazing 30, for example. Call the period 1993-2000 the "Dark Age", something like that. Terrible art, terrible stories, no sales, etc. etc. etc.
I definitely think the era of 1993-XXXX does need a negative connotation to it. I see the turning points of Mid ASM V2, USM #1. Loeb/Lee Batman run as big turning points where stories and art got good again.