No matter how you look at it, Shana and Yuji make a great pair (sorry, Yoshida fans, but that's how it is), but the road to get where they were at the end of the anime...that's the rough part. It took a whole lot for these 2 to finally get together, even being on the different sides of the battlefield, crossing swords, and even having Yuji kidnap Shana to his fortress during a set amount of time. If crossing over to the side of evil and having all Tomogahara at the grasp of his palm isn't enough to make you shake your head, I don't know what is. Yuji went through a whole lot just to get Shana's recognition. Sure it was kind of far fetched on his part, and somewhere along the line, he just went a little bit overboard. Still his love for Shana remains, and you can't deny that. Their final moments on earth before they set for Xanadu confirms that Yuji was still thinking of Shana all this time.
Taichi And Inaba
Inaba and Taichi didn't start out well together. In fact, they were nothing more than friends, and almost everyone knew that Taichi had the hots for Inori. Inaba supported their relationship, but even then, we knew that she had problems letting go. When her true emotions were awoken, she tried to seduce Taichi, and there were many times where she broke down in front of him. She felt that he was the one that she could turn to, and while Taichi did like her to some extent, he was still in it for Iori all the way. It took a lot for Inaba and Taichi to grow to one another, and when Inori finally dropped the ball, it was time for Inaba to step in. She really came a long way though, from becoming a kid to getting kidnapped by a bunch of jerks. I think she deserved to get along with Taichi more than Inori did, but surely enough, we all have our share of feels for Inori as well.
Banri And Koko
Linda deserved to be with Banri, that much is somewhat true, but to some extent, I'm kind of happy that he ended up with Koko. They went through too much by the end of the series to not deserve a happy ending, and during the moment at the end when Banri lost all his memories and forgot about Koko, a little bit of me died. They went through so much, starting off as regular friends and then Koko slowly falling for Banri...everything seemed too good to end with just a shitty memory lost plot device. The two had arguments that seemed silly, they had different thoughts and beliefs, Koko even broke up with him at one point because she found out about his memory disorder. And we can tell, Koko was suffering as she did it, she LOVED Banri to no end, and we're all sure that Banri loved Koko as well. For all that they managed to overcome as a couple together, it'd be a f**king waste for Koko not to end up with Banri.