Spoiler Alert! View the list at your own discretion. You have been warned.
#1 The Sorcerer Michelangelo
As mentioned on TV Tropes, It has been revealed in the movie that in the future, Michelangelo has changed his game from dual nunchaku to using magic.
#2 From N to N
Originally, the Teenage Mutant Ninja Turtle franchise falls under Nickelodeon, however, the movie was straight up released only on Netflix and not on Paramount or the main Nickelodeon Channel.
In the movie, there were other interesting content but were actually cut out. One example of cut content is that when the Krang infects people, the consequences would have led to a much more grotesque and brutal physical alterations, however, the producers of the movie decided to cut it out as it may have some problems with violent censorship.
#4 Baxter Stockboy
According to TV Tropes, Baxter Stockboy was supposed to be included in the future but was then cut out.
#5 Casey Jones’ Appearance
The Casey Jones in the original adaptation looks more like villain, but in the alternate future set in the movie, Casey Joneds looks more of like a good guy. His behaviour and personality are also altered, where in the original he is sarcastic and always acts like a smartass but in the alternate future, he is more formal and serious.
#6 Casey Jones and Leonardo’s Relationship
In the original adaptions and in the original TMNT world, Casey is much closer to Raphael, however, in the alternate future and the movie, Casey talks with Leonardo more and he even has a backstory with Leonardo in the alternate future.
#7 Darker Tone Krang
Unlike the previous TMNT media, Krang in this movie is much more serious and has little to no goofiness in character.
#8 Mute Foot Brute
Mentioned as Actor Existence Limbo on TV Tropes, Foot Brute was muted for yet unspecified reasons. This change is very obvious since previous TMNT media had showed that Foot Brute and Foot Lieutenant loved to banter.
#9 Fan Guessed
On TV Tropes, a few years back, before the release news, fan had already guessed that Krang will be playing his part in the series. The face of the precursor race and the alien interference were hints that Krang would return.
#10 Bloody and Violent
Unlike previous TMNT media, this movie has a lot more violent theme involved like gore and curse words. The movie is much more akin to a “grown-up cartoon” rather than kids cartoon.
#11 Unlikely Ignorance
The ninja turtles, despite having fought demons and villains with super powers, still don’t easily believe in concepts like time travel and aliens.
#12 Cut Disappointments
The execute meddling involved with the movie had some fans disappointed. On the Reddit Rise of the TMNT Official Thread, many have specifically mentioned their disappointment due to some characters or concepts not being present in the show, they mention that if it were added it would have added to the quality and depth of the movie.
Reddit Rise of the TMNT Official Thread