The new upbeat opening was a very strange decision, more mystifying than why they chose the original song in the beginning. From what I understand, the fourth season starting with "Borderland" was going to debut a totally revised opening with the Archer theme and have Bakula recite the opening lines that Shatner and Stewart did, albeit "where no human has gone before". For whatever reason (my guess is they didn't want to spend money on new visuals for the opening), that never came to pass and so the revised version of that Rod Stewart song remained.
I like the third season as a one-off. I'm not sure if it was ever the right direction for the series, but I thought it was worth it just for how it made me care for the characters for the first time. I did not like Archer in the first two seasons. He was just too damned naive to make a believable captain, so I was fine with the direction they took him, making him not only more hardened but self aware that he was going to far and losing something. I do like that moment in "Storm Front" where Silik comments on how he changed and Archer says "not for the better". It's stuff like that that made him come off more like a believable person. No longer in gazelle land.
That said, I think the fourth season really should have been what the show was from the start. That would mean I'd erase the whole Xindi arc, wouldn't it? Yet I like what was brought to the table. It's such a complicated show, this ENTERPRISE. That's why I give it much more credit than VOYAGER, which just never went anywhere interesting beyond a couple of dozen episodes.