WMG page for Terminator Salvation.
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The Movie
SKYNET's apparent foreknowledge comes from the events of the last movie.
By the time John, his allies and the T-X arrived in the facility that SKYNET was "born" and while not powerful or ready enough to initiate Judgement Day until the end of the movie, it was still conscious during the events and could've seen what was going on. John Connor is regarded as enemy number one until Kyle came along because SKYNET remembers watching John cause problems for itself and want to shut it down. The T-RIP is designed to look like Arnold because SKYNET felt using the face of one of John's allies as his executioner was delicious irony. The anachronistic robots led it to conclude some sort of time travel probably happened, and began theorizing. With 15 years of plotting the idea that Kyle could've gone back to father John is possible, but it can't confirm it so captures Kyle instead of immediately killing him; it needs him captive to prove the theory since approaching a Stable Time Loop with a sledgehammer is a bad idea. SKYNET still does the whole "capture John Connor" because it's still a theory and not something it can focus entirely on. Sequels
Robert Patrick's character would have been a colleague of Serena Kogan.
From what we know of what Robert Patrick's character, he would have been a scientist researching cell replication as a panacea/Cure for Cancer, which sounds very similar to Kogan's backstory as a stem cell researcher for Cyberdyne's genetics division who also had the same goals as him. Since Kogan became the visual interface for Skynet, it makes sense if the T-1000 was based on a Cyberdyne worker, especially a colleague of Kogan. The transplant didn't kill Marcus.
it simply put him into hibernation, the fact that the heart was exposed indicates that Skynet didn't deem it something worth protecting, so, by using an alternative power source, like say a nuclear cell from a downed terminator, or a heart from a deceased resistance member, brings Marcus back to "life" allowing him to continue aiding the resistance.