Sure, the ending may not be perfect, but I don't think Yotsuba winning was a good idea.
Of course, I'm not saying she doesn't deserve Futaro, the real problem is her love life is written too easily compared to the other quintuplets' love. She's a character with so little development that it's almost invisible, and her love for Fu from the beginning is something that doesn't convince many readers when compared to the gradual development between Fu and the other quintuplets.
In my opinion, choosing Yotsuba is the one that denies the development and relationships of the other quintuplets that have developed over the course of the story. If you want her to win in a way that everyone can accept, at least give her a arc before the war ends.