Walker: Let me question her about your son. Then you can roast her, toast her, chop her into tiny little pieces and feed her to the birds.
Lord Norinaga: No. I want her to suffer. (00:17:10)
Leonardo: Hey! Where's Mikey?
Donatello: Last time I saw him, he was doing this: AhAhAhAhAhhhh.
April O'Neill: This is absolutely the worst rescue I have ever had.
Kenshin: We wait 400 years, and this Casey is still late.
Michaelangelo: Man, I love being a turtle.
Splinter: Put down your sword, Kenshin. They are not enemies. Only lost warriors, like yourself.
Donatello: I think I swallowed a frog. I hope it wasn't an ancestor.
Raphael: Here they are. The three stooges.
Donatello: Yeah, Larry, Curly, and Moe.
Leonardo: Hey, Tinkerbell. Why don't you shoot us?
Michaelangelo: What if we make a major u-turn and wind up in Godzilla-Land?
Walker: Did you really think I'd make it that easy, you nasty little reptiles?
Michaelangelo: Hey, dudes, check it out! We're in Shogun.
Raphael: Hey, it?s wet-willy time.
Whit: Wet-wadum?
Donatello: Gee, if we die here in the past, does that mean that we don't get born in the future?
April O'Neill: I'm going to find an apartment. I have an idea we're going to be here for a long time.
Leonardo: An apartment?
Michaelangelo: Do they have apartments in Japan?
Raphael: Do I look like a real estate agent?
Leonardo: What about condos?
Leonardo: Michaelangelo why are you wearing boxer shorts?
Michaelangelo: So that the guy who arrives in my place doesn't arrive bare butt naked.
Donatello: You were expecting maybe the Addams Family?
Lord Norinaga: You have come back.
Leonardo: Yeah, we like to drop in about every three or four centuries.
Leonardo: We're turtles, friend.
Donatello: Of the teenage mutant ninja variety, Sleezeball.
Michaelangelo: But, I want to stay here... with you.
Mitsu: You will always be here with me, Michaelangelo.
Answer: Michelangelo wants to stay behind for the same reasons as Raphael: because in that time and place, they are well respected, even revered as heroes. They can live openly and not be banished to sewers or subway stations.
LorgSkyegon
Mikey didn't want to stay behind because of Yoshi but because of Mitsu. Raphael even points out that she's the reason he doesn't want to return. When Mikey says they should stay, Raph responds, "Now, forget about Mitsu and give me the scepter."