I always thought that in the anime, Yuichi and Rika got together. In fact, I remember that there was a photograph of the two them married, so I would have to disagree that they deserve better since they aren't dead or "not together" regardless of the amount of the time they have left together. Coincidently, it reminds me of Ayashi no Ceres since
Toya only has a limited amount of time to live even though Aya is pregnant.
You know which tragic couple deserves better? Jil from Tower of Druaga: Aegis of Uruk. I have no idea what agenda Kaaya has in mind, but I certainly believe Jil deserves together, or that they could went up the tower together. (RAGEEEEEEAJWEFANO#$F!!!!!)
While I'm not a fan of early Gundam works, I do think Kou and Nina from Gundam 0083 Stardust Memory deserve a better future than the shit the producers put them through, and ultimately break apart. Speaking of Gundam, Gundam SEED Destiny, I think what Cagalli and Athrun went through was bullshit. They deserve better.
Speaking of Romeo x Juliet, Basilisk is an anime that uses Shakespeare's template except in feudal Japan with ninja clans instead of houses. I really pitied the couple, and the ending was pretty dramatic.
And as much as I thought Fate/Stay Night was a shitty anime, I thought that Emiro and Saber deserved better.