Ok first off, I'm just gonna say this upfront that this is a personal opinion and I don't care what you ship.
OBVIOUS SPOILER WARNING FOR ALL OF HEROES OF OLYMPUS (and mild Trials of Apollo book 3 spoilers too)
ok so. into my points
if Jason and Leo were together the "to storm or Fire the world must fall" part of the Prophecy would've been SO MUCH MORE tragic. like they both know (at least a small part of them) that one of them HAS to die to defeat Gaea. they both know they're doomed. and that would make every moment they have together even more meaningful.
and don't you DARE get me started on their deaths. I mean, just think of it. the final battle at CHB against Gaea happens the same as canon, except before Leo's sacrifice he Kisses Jason for what may be the last time. an acknowledgment that their time could be up now. Leo still sacrifices himself and everyone thinks he died. Imagine the moments we could've had of Jason thinking of what he had and what he COULD'VE with Leo. what could've happened between them.
and when Leo eventually comes back and He finds out Jason is gone...that he couldn't prevent the fates making storm or Fire fall. Leo thinking that It STILL should've been him. that it was HIM who cheated Death, so it should've been him who permanently died. thoughts that he was never able to see Jason again. that they were never able to know the other was alive. and they could never have their future together.
But, at the end of the day, my opinion is mine and yours is yours