Well let me amend my statement. It wasn't Marcus I had my problem with, it was-
HOLY SPOILERISHNESS, BATMAN!-the fact they built up this new character, so much so that he was more important than Connor, Reese, or the Resistance, and then bumped him off.
[snip]
I guess. Or a little side story (like something you'd see in one of those shorts collections like Animatrix) only it was given feature length. You know what I mean? I'm not sure I'm explaining it right.
I think your problem with it is the lack of consequences. As far as anyone is concerned, Marcus has had no impact upon the franchise apart from this film. He was neither mentioned before nor likely to be mentioned again after this outing.
So, no one knew about Marcus and it took till the events of "Salvation" for him to be "activated".
Bit of a waste. Throwing in a cyborg (rather than the android T-800s) was an interesting idea but kind of like "Cyberdyne were doing cyborg experiments way back before Skynet went live? Okaaaaaay."
SOME THOUGHTS
How did Skynet get involved?
Well, we have to assume that Skynet learned everything that humanity has to offer before/after Judgement Day. This is substantiated by not only having access to all Cyberdyne's old research (T3 states Cyberdyne was bought out by the USAF) but also that proto-skynet had infiltrated the world's computer networks.
We also have to assume that Skynet is either 1) a logical, self aware machine 2) completely insane.
If it is 1, then it HAS to have all the information/facts at its disposal to realise that, travelling far enough along the line of logic, its only solution for survival is to try and kill all humanity which then it learns it cannot do, so attempts time travel to ensure a reality comes about where it CAN survive.
If it is 2, then the writers can literally do whatever they like, without logic and just say "Yeah, Skynet's crazy, whatcha gonna do? *shrug*".
2 is lame and lazy writing. But does mean that all those plot holes and unexplained things, well, there's your answer.
Well, given that Skynet is logical and doesn't want to "die", it decides to eliminate humanity. It forces humans to make better factories, so it can make its better terminators and continue the fight against humans.
In Salvation, Skynet appears to know that John Connor and Kyle Reese will become lynchpins to its eventual destruction.
So Skynet tries everything it can, even in to getting (possibly) the only cyborg in existence to believe its human so it can get close to John Connor and put the latter in to a position where Skynet might be able to kill Connor.
However, again, Skynet's attempts to create it's own reality through manipulation of events (even if Time Travel isn't involved this time), go awry and instead work in favour of its eventual destruction.
Let's consider:
1) It wipes out all the Resistance Command (on the sub) that were against John Connor putting Connor in charge and he's the only one who knows all about Skynet.
2) It also reveals that the T-800s are ready to go online, so that cat is out of the bag ('cause even if John Connor knew that Skynet was making terminator androids, he could never be sure when, Skynet could have got more use out of that surprise).
3) He also got Kyle Reese to John Connor, who wouldn't have got there if A) Marcus hadn't been involved B) John Connor hadn't been manipulated to going Skynet City (Not its real name
).
So, this means that Skynet is not only privvy to the future (how else would it know that John Connor is going to be instrumental in its destruction), it also believes that it cannot win the war against humans (also echoed by the fact that Marcus quite easily disables Skynet's control over him) in the current future (and worse, there have been several different futures/realities that all changed due to the influence of Time Travel*).
*Terminator, Terminator 2, Terminator 3 and Salvation