These character designs are so good, especially Splinter, and the dynamics sound so good. Imagine, if you will:
-Kakashi and Leonardo, the leaders in blue. Imagine Leonardo being a big fan of Kakashi and trying to learn from him, but at a certain point, he saves Kakashi's life through his own unique talents. They have also both used swords, and Kakashi still uses his Lightning Blade, which is a bladed weapon.
-Sakura and Donatello, two nerds with vaguely similar colors. They're the smartest ones on their teams that aren't sensei, and there's likely some comedy around them having more common sense than the next 4. They're also both supports, and use bludgeoning weapons.
-Sasuke and Raphael, "cool but rude," two guys with red on or around their eyes. They're both the edgelords of the group, and are notable for being quite angry, but secretly caring. They also both use cutting and piercing weapons or techniques.
and finally, my personal favorite idea for a combo:
-Naruto Uzumaki, "Konoha's Orange," and Michelangelo, "The Party Dude." While both being tricky little pranksters, and both being treated as the least intelligent, they also have the most unconvential fighting style, and both use a spinning weapon or technique for bludgeoning.