Cyrus x Schala: Must be my Chrono Trigger OTP. Despite of the fact that the characters haven't met in the canon and that they are from deferent time spans, I think it would have some chance. You see, they both share similar pasts and fates. Cyrus was the most important knight of the Guardia Kingdom and was he hero of legend; the first warrior to bear the Masamune (since the first PERSON to bear the sword was Melchior, the creator...). Many people looked up at him and even Queen Leene (this is a popular fandom speculation) seemed to have something going on with him. Cyrus dies in the hands of Magus (Janus), King of the Mystics (Fiends); this was because he wanted Glenn (his squire) to run to safety and take care of the kingdom. Because Cyrus sacrificed himself, Glenn manages to survive, of course, having been turned into Frog. This means that Cyrus was a real hero who gave his life away to save his loved ones.
Schala is the princess of the Zeal Kingdom and she was was in charge of powering the Mammon Machine up; a very important fact of the game. Since her mother, Queen Zeal, had been possessed by Lavos (the main antagonist in the game), she had lost all of her sanity and made her people (the Enlighted ones, magic users) think that they were superior to the Earthbound ones (people possessing no magic. They were exiled to live in the Ice-Age lower land). However, Schala (and the Gurus) keep their kind personalities. Schala is threatened by her own mother; the queen says that if she doesn't cooperate, she will kill her and her loved ones. Because she has no other way, Schala is forced to work for her mother. When Crono and the party want to kill Lavos and destroy the Mammon Machine in the Ocean Palace, they fail and Crono is murdered by the beast. Just as the Ocean Palace is about to collapse (it is more than a thousand feet underwater!), Schala sacrifices herself; she uses her last amount of magic to save the remaining of the party and the Prophet (Magus in disguise; who is actually Schala's long lost brother, Janus) and stays in the crumbling palace not to be heard from again until Chrono Cross/an extra ending in the DS version of the game.
I think Cyrus and Schala would make a decent couple because both of them are noble, kind-hearted, brave and, like I said before, they share similar lives.
Frog/GlennxLucca: I will get eaten by the LuMa fans but I'm willing to take the risk

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I like this couple very much because their interaction in the game are so funny, dramatic and unique. When in the Cathedral in the Middle Ages, a Nagaette appears and attacks Lucca, sending her flying. Because she was wounded and Crono was too slow to take out his sword, Lucca's life was in danger. But then, Frog jumps in and kills the Mystic before it can harm Lucca. Lucca scream since she is scared by Frog's appearance (Lucca hates frogs Dx). However, they are forced to work together to rescue Queen Leene and rescue Marle. Once they return to the palace, Frog leaves; says that Crono is an excellent swordsman and that Marle indeed looks a lot like the queen but says NOTHING to Lucca. After he finally leaves, Lucca resents the fact that he didn't say goodbye to her and says "Froggy... Your weren't so bad afterall." (or something like that...).
During the whole game, if you keep them in the same team, their dialougues are pretty connective. And in one ending (if you decide to kill Magus and didn't revive Crono to fight Lavos), the rest of the gang and Gaspar appear in the timegate and Frog is Human again (Glenn). Lucca just stares at him and when she realizes that it was Frog, she begins to fangirl saying "Wow, Glenn! Who would've known you were such a dish?!"
MagusxFlea: Ok purists, I'm going to disrupt the canon here. For me, Flea will be a FEMALE and so, I'm gonna refer to Flea as such.
This is mostly because of fanfiction and I decided to agree with it. When little Janus (Magus) arrives to the Middle Ages via Time Gate, Ozzie kidnaps/takes him in. Janus was the prince of Zeal but knew NOTHING about magic. So, who taught him magic? many speculations say that it was Flea since she is a general in the Mystic army and she is a well experienced magician. Later, when Janus becomes Magus, and the king of the Mystics (Taking over Ozzie's role), Flea is sent to spy on Crono, Frog and the other party member (this one is optional; I mostly go with Lucca because I need fire magic) and disguises herself as a bat. Once she is defeated (in her true form, of course), Flea calls out Magus' name and disappears.
Once the gang return to the Middle Ages (side quest), and if Magus goes too, Flea gets very angry (as well as Ozzie and Slash). After the Mystic Trio is defeated (in my case, I never hurt Flea and let her run away because I'm a crazy fangirl like that...), Ozzie locks himself in an Ice shield, where he can't move a single muscle. There are switches to open the trapdoor underneath the imp, but before the party could guess which switch it is, a yellow cat just walks in, presses a switch of Ozzie's trap door and leaves. Many people like to think that the cat is Flea since she is the only one who can shape-shift (well, Yakra too, but Yakra was killed at the beginning of the game, so he doesn't count).
I mostly see this as one-sided, from Flea's behalf xD