While we're on that subject, I think all of the "half" episodes are quite weak. Their incredibly short running times mean there's not much time to develop a proper plot.
The Origin of Dr. Viper as you say feels too rushed, and has a weak resolution. Volcanus Erupts! and SWAT Kats Unplugged just feel like "basic" episodes going through the motions. Cry Turmoil is the strongest in terms of story (even if I'm not biggest fan, I can admit that), I think, but again, it's just way too short. I think they should've dumped Volcanus Erupts! and SWAT Kats Unplugged and expanded The Origin of Dr. Viper and Cry Turmoil into full-length episodes. This would've allowed for developing T-Bone and Turmoil's relationship better, as well as giving her an actual backstory of some sort.
I also feel that making The Origin of Dr. Viper entirely a flashback episode without a wraparound story set in the present was a mistake. It feels out of place in season two as a result, and adding a prologue and epilogue was something they could've easily done if it'd been a full episode.
Of the full-length episodes, I actually think two of the most popular, Mutation City and The Deadly Pyramid, are very weak. Both have very good animation and a fun central premise, but their stories don't quite seem like they justify the expensive animation boost (except for maybe Mutation City). They also drastically underuse their main villains. Dr. Viper barely shows up, and it's his only season two episode that isn't a flashback, while the Pastmaster doesn't do anything particularly interesting except for wear a cool crown. Also, his motivation seems weird; prior to realizing Callie looks like Callista, he was sending the mummies to kill Mayor Manx, someone he's never even interacted with.
Why does he want to kill Manx? So he can be mayor? If so, why? His schtick is he wants to return everything to the dark ages, and he doesn't need to be mayor to do that, or even actually do anything to Manx in particular. It's like Glenn Leopold wanted the plot to involve the Pastmaster using Callie as a substitute for Callista, but was just spinning his wheels, story-wise, prior to the scene where her glasses get knocked off, and attempting to kill the Mayor was the best thing he could come up with to have as the Pastmaster's initial plan.
In general, I think this speaks to a problem the writers had with the Pastmaster - namely that they didn't quite seem to know what to do with him half the time, and nowhere is it more apparent than in The Deadly Pyramid. Other strikes against it are the fact the mummies, big though they are, don't have particularly interesting character designs, and "killing" Cybertron. I'm one of the people who liked him, and I disliked the episode's mean-spirited treatment of the brave little robot, and the somewhat bleak and ambiguous ending he gets. It would've been nice if Leopold had let Hackle successfully rebuild him.
As for Mutation City, the mutants are cool, especially Viper's gigantic form at the end, and it has some good story moments, but as I said, Viper's barely in it. Admittedly he only had a couple of scenes in his debut, but they were strong ones and quite memorable, so he left an impression. Here, he pours some pink slime on a frog in a pet store, then pops up briefly to gloat later, and then suddenly is a hundred feet tall... and as awesome as he looks as a giant, he doesn't do anything particularly interesting, besides shoot acid out from under his fingernails (which is more weird than cool), and smack Enforcer Headquarters with his tail a couple of times. Oh, and he gets taken out like a chump. Also, the "T-Bone can't swim" and "T-Bone gets mutated" plot points are poorly developed, and Mutant!T-Bone, like Giant!Viper, doesn't really do much.
I'll say this much, though, at least they endangered the right SWAT Kat this time. I found it a little weird that in The Ci-Kat-A, while T-Bone has the bug phobia, he isn't ever put into any situations wherein he confronts it or even really overcomes it (bar one line at the end as a joke). If Mutation City had followed The Ci-Kat-A's example, it would've introduced the fact T-Bone can't swim... and then never done anything with it, victimizing Razor again instead.
R.I.P. Gary Owens (1936-2015)