Actually, on second look at the OP, it says:
Originally posted by FrothByte
...So Skynet decides to break the truce, invade the domain controlled by the Matrix, and attacks Zion with every robotic force it has...The Matrix retaliates by sending all of it's sentinels against Skynet...
Unlike my prior argument for the Matrix winning (just a vastly superior AI), I am now considering these factors...
1. Skynet strikes first. First strike always presents opportunity for advantage, but Skynet is striking Zion, not the Machine City. Advantage could well be squandered with a wrong first target.
2. There is no mention of hacking as a tactic: they fight hardware vs hardware, a clash of robotic infantries. Therefore, hacking is not permitted in this fight (?), which I saw as the Matrix's big advantage: a bigger intellect simply overpowering a smaller one.
3. Also not mentioned in the OP: use of EMPs, which the Sentinels were extremely vulnerable to. Are the Terminators as vulnerable? In any event, since they're not mentioned in the OP, EMPs are not allowed (?). Another potential advantage to Skynet lost.
4. Time travel: also not mentioned in the OP, which is another, potentially big loss for Skynet (like the EMPs). Otherwise, the perfect first strike would be to send a Terminator back in time to keep the Matrix AI from being built in the first place. This might also automatically eliminate the Zion problem (but if there's no Zion problem, then Skynet would not be tempted to strike first, in which case the Matrix and Zion could come into existence, in which case...)
Basically, given a literal take on the OP stips, now I'm not sure who would win. But if all advantages were allowed, I could see Skynet taking this, mainly because of a potentially game-ending first strike at the right target via time travel. If any clean-up operation was required, then EMPs could be used.
But as stated by the OP: I just don't know. Maybe still the Matrix, because all Sentinels can fly (HKs can, but not Terminators), they're fast and agile, and they may hold the numbers advantage.