As for the history of changing out characters:
Originally, Joel's concept was that he was the last man on earth, and was in a spaceship, trying to come in contact with any other survivors (shades of I Am Legend). So he won't get lonely, Joel built some robot companions. Eventually, this idea was changed to Joel originally working as a janitor for mad scientists Forrester and Ernhartd. The Mads needed a test case for their experiment, so they blasted Joel up into space. The experiment: send Joel cheesy movies to see how many awful flicks it takes to drive one's brain insane. In order to keep his sanity, Joel and his robot pals riff during the movies.
After Ernhartd went "missing", Forrester hired a former Arby's employee named Frank (or TV's Frank). Later in the series, Forrester and Frank hired a temp worker named Mike. Gypsy overheard the two Mads talking about killing Mike, but misheard, and thought they were talking about Joel. With the help of Mike, Gypsy prepares an escape pod for Joel. After Joel leaves, the Mads need a new test case, and so they conk Mike on the head, an shoot him into space.
Unlike Joel, who treated the bots like a surrogate father, Mike was more of a buddy to the bots, somebody that they could pick on, but still pal around with. In addition, Mike had more of an average Joe persona, while Joel's was more laid back.
Later, TV's Frank was summoned to "Second Banana Heaven". Pearl moves into Forrester's place in order to look after him. At the end of season seven, Forrester's funding is cut, and he plans to end the experiment and move back in with his mother and cut loose the Satellite of Love (the spaceship). However, Mike and bots manage to find a way of escaping, and head back to earth. The episode ends with Mike and the bots becoming pure enery (as they're at the edge of the universe). Meanwhile, in a hilarious parody of 2001: A Space Oddessy, Forrester tries to grab a giant videotape labeled "The Worst Movie Ever Made". Ultimately, he's reborn as a star-baby. Pearl sees this as an opportunity to try again at raising her son.
When the Sci-Fi era begins, Mike and the bots learn that they have been traveling for centuries, and our now heading back towards earth in the year 2525. Much to their shock, earth is now ruled entirely by apes, one of whom is Prof. Bobo. As demanded by earth's new ruler (which is later revealed to be Pearl), Bobo sends the guys another bad movie to watch. It's soon revealed that Pearl gave up on raising her son, and smothered him to death with a pillow. His dying wish was that Pearl take over the movie experiment. Thus, Pearl froze herself and woke up in the year 2525, becoming the ruler of the apes. Earth gets blown up, but Pearl and Bobo manage to escape. They land on another planet ruled by "observers". It, too, gets blown up, with one survivor, Brain Guy. Eventually, Pearl, Bobo, and Brain Guy reside in a castle known as Castle Forrester.
During the last season, Joel returned for a brief apperance. He manages to save the SOL just as it was getting ready to be blown up (Dr. Forrester had it set to do this earlier on). And for one brief moment, Joel and Mike finally meet. Frank also appears. It's revealed that Frank was kicked out of Second Banana Heaven, and eventually became a Soul Taker.
At the end of the series, Pearl accidentally sends the SOL to crash back on earth (even though earth had already been destroyed, but who cares? It's just a show). Pearl gives up on saving Mike and the bots, and gets a job as dictator of Qatar. Brain Guy and Bobo are also getting new jobs. Mike and the bots finally crash on earth, and Mike, Crow, and Servo rent a small apartment (Gypsy started "ConGypsoCo", and opted not to move in with the guys).