When I learned that Series 5 was going to be a prequel, I thought it was a bad idea, mainly because (just like the Star Wars prequels) I had my own preconceived notion of what the time of the founding of the Federation would have been like, and there was no way that the present lot at UPN was ever going to deliver what I wanted. And I'd bet that a LOT of other fans felt the same way.
To be fair, the show makers can't be held accountable for the fans preconceptions about what they'd theorized must have happened in Federation history. I mean, realistically as you've identified this is the real problem ENT encountered all along: that a lot of things that we'd assumed
over the years, but which had never actually been confirmed on-screen, suddenly turned out differently to how we'd all imagined them. It's no wonder fandom found it difficult to overcome that...