I couldn't agree more. 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. Plus, as you say, the whole tone of the show made it look more like a TNG prequel (actually more like a continuation of VOY, only with a different ship and a different crew, and the time period was irrelevant). We got the Borg, the Ferengi, the Nausicaans, Risa, Holodecks, Klingons, Nemesis-looking Romulans and Remans, and a ship that looked like one of the First Contact background ships. Absolutely nothing that even remotely screamed "TOS prequel."
Those nacelles on NX-01 were pure TOS. And the old communicators and sound effects. And T'Pol's Spock Scope. All token stuff though. Five minutes into "Broken Bow" I realized this wasn't the prequel I was expecting. I just tried to enjoy it for what it was - and IMO it was at it's very best when they said "fuck the timeline!"* and did the Xindi mission. *Then season four comes along, with so many prequels and tie-ins one has to assume all those changes led TO the Trek history we know, rather than away from it.
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...
But that was the entire problem. The only reason why Series Five was a prequel was because they had run out of ideas for what a Star Trek show should be about. Some UPN suit decided that, "hey, it worked for Star Wars, so let's do it for Star Trek!"...even though the jury's still out on if it actually "worked" for SW. But that's a whole other story. If you're going to make a prequel to one of the most beloved and popular television shows in history, then you have to do it because you love and honor that show, not because you've just run out of ideas of what to do. That's the mentality of Hollywood at present, producing shitty sequels to hit movies from thirty years ago because no one has an original bone in their bodies (or remaking hit movies with soulless replacements). In the case of ENT, the executive producer himself claimed to not have watched TOS. Really? The show you're making a prequel of, you've never seen? There was all kinds of backstory to the formation of the Federation, whether it was the old FASA roleplaying games, or the licensed Trek novels of the 70's and '80's. Granted none of that was canon, nor were they obligated to follow it, but they could have at least done some research. But the show was never really about being a TOS prequel. It was about being a prequel to TNG and VOY, and not a very good one at that. It was more like a prequel in name only, as most of the scripts, characters, sets, props, ships and aliens could have been used for the 8th season of Voyager. By the time they figured that out, they did a 360 and went completely overboard with the TOS references. But by then it was too late. I'll have to take your word for that, since I stopped watching the show halfway through the second season because I thought it was crap, only to resume watching around the fourth.
I think ENT's most basic problem was simply this: They'd been doing it too long. I mean, by late 2001, when ENT premiered, Rick Berman had been on since TNG Season One in 1987 -- fourteen years. Branna Braga had been on since, IIRC, TNG Season Season Four -- eleven years. On top of this, both were under intense pressure from UPN executives to keep ENT according to TNG-style formula, to keep from experimenting creatively and innovating, to keep Star Trek from evolving along with the rest of the television medium (which was, after all, just starting to enter the Modern Golden Age of Television, with programs like The Sopranos, The West Wing, and Six Feet Under all being contemporaries of ENT). So when you combine these things, you have a recipe for creative stagnation. It's really no wonder that it took Manny Coto, with his willingness to innovate a new storytelling style (successive three-episode arcs), his willingness to embrace Star Trek's political heritage (e.g., the Vulcans planning to invade Andoria on false allegations of their developing a Xindi WMD as an obvious allegory for Bush invading Iraq), his fresh take on how to link ENT with TOS, and his over-all sense of fun, to make ENT such an enjoyable show in the fourth season.
I think the episode was one of Enterprise's best episodes. It's over the top fanwank, yes. But that's better than most of the series. I'm not a fan in general of fanservice, but that's better than not paying attention to the fans at all like in the first two seasons. When I heard the fifth Trek series was a prequel I was skeptical but I was also excited to see the events that formed the Federation. Instead I was treated to a lot of bland TNG-rehash stories where a character overcomes his character flaw then forgets the lesson in the next episode, then everybody sits in the decontamination sauna. Season four was what I expected season one to be.
This interpretation does resolve a lot of problems I had with the series, at one point thinking it must be set in some alternate universe entirely.
Add to that the ship was being operated by a undersized crew, they were likely running the ship solely through the automatic systems and given their unfamiliarity with the equipment wouldn't have been able to perform battle repairs. Would a "pack" of world war one cruisers be able to destroy a single modern cruiser operating under similar handicaps? Yes.