For Hiro, I voted for Charlie. In my opinion, that has been the best relationship the show's done, though it was cut short.

For Peter, I voted for Simone. Not that I especially liked the relationship, I just think it worked better than the others. Caitlin didn't seem as believable, and the thing with Elle was a bit of a one-sided thing, not a real couple as I see it. Well for Future Niki, we didn't get to see a real good amount of that relationship, though it did seem there were some issues due to the dark path the future had taken. That aside, there is potential I guess, but it doesn't really fit with present Peter. Niki seems to have better chemistry with Nathan.
I voted Heidi for Nathan. She was his wife, though Nathan was disloyal with Niki in season 1. It seems to me that Nathan had found a really good relationship with her, but the results of all this power stuff has complicated things, driving them apart. In season 2, it seemed that Nathan was wanting to make progress to getting his life back and becoming a good father again. Though, if that doesn't work out, I could see him ending up with Niki at some point. As for Meredith, there was something significant at some point, but Nathan's moved on for the most part.