Lothor says they can't attack the Rangers in their civilian form because a Ranger's powers can only be destroyed when they're in Ranger form. This makes sense, as if they just killed them, their powers could be given to someone else. Destroying the powers themselves is a much more effective way to permanently claim victory.
Sensei's body-swapping in "Sensei Switcharoo" offers a two-fold: first he's switched with Shane. When Sensei was a student, as shown in the "Samurai's Journey" trilogy, he was a student of the Air discipline; very fitting. However, when he ends up in Dustin's body, it adds a touch of irony, given that it was his brother Kiya (Lothor) who was an Earth discipline student.
Why Lothor went from a serious villain to a more comic relief villain makes since if you remember his Fourth Wall Awareness. In other words, he knows what happened to Lord Zedd. After Zedd's first appearance, parents complained and thus he was toned down to make him less scary. Not helping that he also knew that he was on a Disney kids show, thus there was a chance that he would suffer the same fate, if not worse. So he decided to invoke his own Villain Decay before Disney could do it themselves.
The minute you realize that Lothor's plan the entire season was to fill up the Abyss by having his monsters defeated, you see the entire season in a new light as one long grand Xanatos Gambit that nearly worked and makes Lothor one of the most brilliant villains in the history of the franchise.
In-universe, the lack of a Wild Force crossover is actually explained by the ending of that series: Princess Shayla takes away the rangers' morphers and jackets. Since the Animarium isn't exactly accessible by normal people, odds are that by the time Princess Shayla was able to reassemble the Wild Force Rangers, the Ninja Storm Rangers would've been able to handle any threat on their own.
If Lothor attacked the Thunder Ninja Academy and captured the other students and their sensei, then why the hell would Blake and Hunter trust him, let alone believe a word that he said? Well, you have to keep in mind that Lothor is actually Sensei Kanoi's identical twin brother. Not only would this fact alone make it somewhat easier for the Thunder Rangers to trust him, but as revealed in the Dino Thunder team-up, Lothor is able to flawlessly disguise himself as Kanoi to convince the Wind Rangers to put on corrupted morphers. This makes it a strong possibility that he used this ability to convince Blake and Hunter he was telling the truth (e.g. Lothor could have posed as his brother when he killed Blake and Hunter's parents, and had one of his minions record it to provide false evidence, etc.).
Lothor was shown to be in the earth class during his days as a ninja student at the Wind Ninja Academy. In the series finale, he is defeated by being sealed in the Earth.
In "The Wild Wipeout" Tori ends up in a Mirror Universe where the Rangers are evil and Lothor and his allies are good guys. If this is a Mirror Universe of the main Power Rangers universe, does this mean that evil versions of other Ranger teams exist the Mirror Universe too?
