Now, I'm schmoopy. I would have loved to have them remain partners. I always look at new series with a slashy eyes, looking to see if there are two males who I can dream about. That's one of the reason that I only watched the X Files when I happened to remember it was on before Krycek.
I also hoped that they would one day end up working for the same side and learn to be partners. There are some good stories with that idea. Tons of them.
I like the ones where Alex is reinstated to the FBI and I like the ones where Mulder goes rogue to be part of the resistance.
If Alex had gotten smart early on, he might have told Mulder and Skinner everything and then life would have been very different.
I would have love to have seen Scully with the two, trapped in a bureau car with the two arguing like demons! I bet she would have boxed them on the ears!