I'm not saying that SUPERBOY season 3 and 4 didn't have good individual episodes. Far from it. The examples you list are good ones. I love parralell universe stories. I just prefer the college setting of the first two years as opposed to the office setting of the last two.
The setting isn't as important to me as the quality of the writing. The first two seasons were frequently quite dumb and inept, and the plots were superficial, pure action with little character development. The latter two seasons (renamed
The Adventures of Superboy, and practically a whole different show) were far more intelligent and really dove into the characters.
Also, the treatment of Lana in season 2 was sexist as hell. I mean, I admit I loved how often they put her in bathing suits, but she was constantly being sexually objectified and harassed, both by the villains and by Clark's obnoxious new roommate, and it was tiresome. She got to be a much stronger, more dignified character in seasons 3-4.
As far as the setting goes, I find it amusing that they were basically doing
The X-Files before
The X-Files existed. The set design for the Bureau of Extranormal Matters was also strikingly similar to
Smallville's
Daily Planet sets quite a few years later. I do wish they'd given the new supporting characters more development, though. It was nice that they finally had a regular black character, but he only got one focus episode in two years.
In the case of LOIS & CLARK, I thought the show degenerated into a soap opera in seasons 3 and 4 once Lois discovered Clark was Superman. I realize it was really supposed to be that all along, but it was really played up in the last two years to, in my opinion, the shows' detriment.
Again, I think the key isn't the concept, but the quality of the execution. Seasons 3-4 were done by new showrunners who didn't seem to respect the material and turned it into a farce. If the same storyline had been done by season 1's showrunner, or even season 2's, it would've been much different from what we got, and probably somewhat better.
Superboy changed showrunners in season 3 too, but in that case it was a change for the better.