I usually assume that both parties have equal numbers but here it would seem illogical since there are obviously more Humans in Zion than in the bunkers on Terminator Earth. Since most of those people in Zion are probably not military personnel, the number is actually lower but still more than on the Terminator's earth. Not only that but they have more stuff are their disposal, ex: hover ships, APU's, emp's, etc. To answer the uncertainties that I had and that you the reader may have, Neo is part of the rebellion so yes he is being considered but keep in mind that outside the Matrix he really has no power except maybe his martial arts skills. He does have the ability to blow up sentinels and sentient bombs but that is because they are connected to the source, meaning that any technology that the Humans from the Terminator universe have is safe from that. John Conner and his wife have both reprogrammed a T-101 for their own use so they can be included (although they were sent back in time they were still part of the rebellion and I will allow their use here). John Conner is a better strategist and tactician than that Locks guy. John's army beat an almost impossible enemy that had them totally out numbered and out gunned, that weighs heavily on my decision here just as it did in the Matrix vs. Skynet battle. The humans from the Terminator universe had to be more agile and cunning than the Terminators and Hunter-Killers, therefore I believe them to be more than a match for a fleet of APU's. The hover ships will however be able to mow down some of John's troops but not more easily than a Hunter-Killer. Having one or two Terminators won't be much of a big deal, especially since the Matrix Humans have those energy weapons that can take out a sentinel, thus the Terminators are easily taken out. Zion is an underground base, so the Terminator HUmans won't be able to reach it on their own. Like I said, John is a wicked tactician, he will be able to come up with a plan to defeat the Matrix Humans. Since they have the ability to take out a hover ship (I mean they take out Hunter-Killers that have armour, so a flimsy ship running on weak hover pads should be no problem), I think that John would want to gain control of one much like he took control of a Terminator. So his guys take a couple of ships and APU's, storm the gates of Zion and release an emp to knock out all there defenses. Then his guys come out of the downed hover ships and take them down with there regular assault riffles (assuming that their usual pulse riffles would also fall prey to the emp). All the crap that the Matrix Humans have is nothing new to John Conner, he beat a whole army of robots with the crap that he has.
Winner: Human Rebellion (Terminator)