While in some ways I agree with you, I am not sure what part of his alibi is so ridiculous. It also does not strike me as odd that he would think he was the prime suspect, even before it was officially announced as a homicide. At the point of the interview she had been missing for at least a week, of course he would think all eyes would be on him.
On the hot new girlfriend, they had been dating for a few months by this point. That's all I can really find as far as factual information, and it seems neither one thought it was that serious. I can find no hard information that states she told him she didn't want to be a step-mom.
Phone pings referenced on the Study facebook page are only an if. Main point is we don't know when her cell phone last pinged. We don't know what pings occurred before the last ping either.
Sure, he does seem the most likely perpetrator of this crime, I can agree to that. However, someone with intimate knowledge of where she was going could have easily committed the crime and scattered evidence to make SC look questionable.
Ok... Here's my pure speculation: Maybe SC wasn't really the father. Maybe it was someone else who had something to loose if it came out who the father really was. Per SC interview, I got the impression that he was not fully convinced he was indeed the father. My guess is he would have wanted a paternity test to prove this was the case. Where would eyes have turned if he wasn't the father? Once again, unfounded pure speculation.
Just trying to examine all possibilities.