Here is a list of reasons why Minako and Zoicite should be together... in no particular order.
Warning: This section contains spoilers!
Common goals and past?
While watching act 35, it was clear to me that Minako/Venus and Zoicite had a lot of things of things in common. Out of all the Senshi and Shitennou they were the ones most concerned about the past and preventing it from repeating itself. At the same time they were both very loyal to Usagi and Mamoru, although that goes for all the other Senshi as well. But both Zoicite and Minako concentrated most on the past and their mission, making them team up in act 35 and exchanging favours. In that episode I seemed to pick up hints of Zoicite and Venus being involved in their pasts, especially in the scene where Zoicite and Kunzite talking about Beryl and Minako's line before dropping the music box on the floor. (The transcript of that episode can be found at Shingetsu.) It seems that both Zoicite and Minako have something about their past life that isn't revealed and to me it looks like they were involved somehow. (With Zoicite somehow understanding Beryl dragging her unrequinted love to the present and Minako saying that she knows what it's like to forget.)
Zoicite's obsession
When everyone believed Venus to be the princess and when Zoicite was searching for her, he also seemed to have a weird obsession for her. Jedite and Nephrite also had their assignments from Beryl (Gather energy and find the Silver Crystal) but they never seemed quite as obsessed as Zoicite was with his. He was constantly on Minako's trail with his music following her. One example is in act 8, when the stereo in Minako's car suddenly starts to play Zoicite's piano music and she sees him in the car window, reaching out for her with a very creepy look on his face. If finding the princess was just an assignment from Beryl, then why was Zoicite so obsessed about it? This would go nicely along with the theory that Venus and Zoicite might have been involved in their past life. Like Mamoru and Usagi, the connection or pull could have carried on to the next life.
Connection
I know I'm risking sounding like a hopeless romantic, but to me Minako and Zoicite simply seemed to connect during act 35. They were partners and attempted to seperate Usagi and Mamoru, but they seemed to have a great understanding about each other. Their talk on the rooftop after their brief fight is anything but hostile, even though they clearly know that they are on different sides. There is also a long look exchanged between them while both of them are quiet. Also, in act 46 Zoicite ends up being stabbed to death protecting Sailormoon. The next moment Venus, Jupiter and Mercury are shown fighting a youma, with Venus being focused on more than the others. When the youma is gone, Venus tries to go after Sailormoon but as she runs she starts to feel a pain in her head. Cut back to Zoicite and he's falling down because of his wound. Cut back to Venus and she's falling down as well because of her illness. It all seemed too much of a connection between them to ignore. Also, like Zoicite Minako died only after turning around and choosing the present instead of the past.
Similarities
Both of them had a strong interest in music, Zoicite using music to channel some of his powers and singing simply being a part of who Minako is. A more morbid similiarity is that out of all the Senshi and Shitennou they were the first to truly die (Nephrite becoming mortal and Makoto just almost dying in that 'OH! NO!' cliffhanger in act 45.). Also, both their death scenes were done with music (Zoicite playing the piano to reach out to the other Shitennou and Minako singing before reading her farewell letter.)
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Anything missing that you feel should be here? E-mail me with reasons why Minako and Zoicite should be together and I'll put your reasons here with full credit.