I’d say it is kind of a toss up between Misaki and Saki. While Saki definitely has the better written scenario, both Misaki and Saki fit in that they have a past history with the protagonist that involves the Snow Sakura. (In fact, they use the same “girl with no face” image when the character’s past with you is revealed.) While my personal preferences tend toward Saki, to me the actual ending (as opposed to the scenario leading up to the ending) and other evidence favors Misaki as the “true” heroine.
When I played, it seemed like Saki was the true heroine to me. Her recollection of the past events closely match up with what was shown in the beginning, and Yuuji seemed to have remembered them happening as well. Other people I know seem to vote Saki as the true heroine.
I think with the case of Snow Sakura, it has two endings of equal strength as “true” endings, while all the rest could be considered side stories.
I tend to agree that multi-branch games rarely have a true ending. Of those that I have played, only Figures of Happiness and Heart de Roommate offer an ending that clearly is meant to be the “true” ending. Crescendo comes close, but it just doesn’t quite have the authority behind it as the other two do.
Considering there’s no less than 3 yandere in Nozomu’s class (Kafuka, Chiri, Mayo) - I’m not quite sure even FAILING would mean Nozomu should live. Chiri and Mayo would do it out of spite if rejected. Plus we still don’t know the entire roster of Class 2-He - for example Kanako, Shouko, and Miko are new to the manga and have yet to make a real anime appearance (they get a quick cameo in the fast shown pics starting @ 0:32) - so only the gods know how many more nutjobs are in love with their teacher.
Nozomu is screwed. Suicide or not… he’s going to die before graduation. 
But Kiri and Mayo seem to get along fine… so Narg thinks a threesome with them, should make it worth the violent death. 
Now that I think of it, Kana - Little Sister’s true ending is also one that could be debated. Out of the 6 total endings, the 3 Intellectual endings build off of each other sequentially. And oddly enough the last of those 3 (or rather the 6th ending) has an extra epilogue tied to it that none of the other endings have, not even the so called “Best Ending”.
And don’t forget the special scene in the game Crecendo where the character can watch a movie based on the events of Kana, but using the events of the Intellectual ending.
These two pieces of evidence leads me to believe that Kana dies. But because she donates her liver, her cousin Cana - a character completely ignored for some reason in the “Best Ending”, yet alive and well in the Intellectual epilogue - will survive.
I still say a few others are possible.