Later seasons weren't really convoluted: season 3 was a year-long storyline because one of the incoming producers worked on 24 - I imagine he must have been delighted to leave that show after 7 years only to be told what they'd be doing with Enterprise - though most episodes up until the final third of the season were relatively self-contained apart from the "looking for the bad aliens" premise, while season 4 had a bunch of 2 and 3-part episodes.
I came around to the show many years after it had been scrapped, but I remember originally giving up on Enterprise with the season 1 finale: Captain Archer has been Quantum-Leaped into the future and the final shot is him staring into the camera just like he used to do before the title sequence on Quantum Leap, and he doesn't say "OH BOY"? At that moment, I knew this show was bullshit. Later, the writers would admit they actually wanted to do this, but the producers didn't want to end the episode on a light note. Another thing writers revealed about the "temporal cold war" story arc was that the mysterious figure from the future talking to the space-terrorists was going to be revealed to be an older, nameless character who would also be played by Scott Bakula, and if you look at the design of the "communicator" the future figure used to talk to the space terrorists, it's clearly the Quantum Leap Accelerator with a glass wall around it: the writers had written the main villain of the show to be Sam Beckett from Quantum Leap without telling the producers. BRASS BALLS right there.