From beginning to end, this movie is a love letter to the Teenage Mutant Ninja Turtles franchise and its fans, ends with a live-action segment showing Turtles creators Kevin Eastman and Peter Laird (who are played by actors but voiced by Eastman and Laird themselves) circa 1984, as they take a break from creating the first issue of the franchise in order to take lunch, speaking about how satisfied they are with the comic book and how they hope it will sell. Not only does it bring the whole franchise full circle, making it the perfect ending to a movie that celebrates all the incarnations of the turtles, it's also a touching tribute to the franchise's creators.
The 2003 and 1987 turtles part ways and trade each other's catchphrases as a sign of respect.
1987 Turtles: It's Ninja Time!
2003 Turtles: Turtle Power!
Related to above: Raph didn't admit it until they were gone, and, although he tried contradicting himself right afterward, the smile on his face told us otherwise.
I'm gonna miss those fudgeballs...not.
Earlier than either of that:
2003 Leonardo: Today, we're more than just allies. We're brothers.
In the same vein, there was one line from Splinter before the two teams really started getting used to one another. It was directed at the two Dons, but it would have the same effect with any of the counterpart pairs:
Splinter: Well done... my sons.
And, in a sense, the Mirage-Turtles' final thoughts on their adaptations.
Mirage Donatello: I'm gonna miss those wannabes.
Mirage Michaelangelo: Yeah, I kinda dug the initials on the belt-buckles.
Mirage Raphael: Huh. You would. I could go for a slice, though.
Mirage Leonardo: There's that place on Bleecker.
There was also the portrayal of 1987 Splinter. He escapes any of the Take Thats and is portrayed and treated with great respect and dignity.
1987 Splinter: Please take this moment to nourish your body and soul, as you prepare for the challenge that lies ahead of you. 2003 Leonardo: Thank you... Master. My brothers and I have found your dimension to be, well, disorienting. But being here, seeing you feels right. 1987 Splinter: To me also, Leonardo. You four are welcome here always.
Both Splinters are treated with great respect- the 2003 one gets angry when the 2003 turtles start picking on their 1987 counterparts. No matter which world, the Splinters don't see "Otherworldly Copies," They just see eight sons.