Jim is a great actor, we all know that, and he doesn't go about things the "boring" way. So why did he pretend to be Mollys boyfriend to get close to Sherlock, when she isn't the closest person to him and way too easy to manipulate?

In this verse, he didn't. Instead, he meticulously planned every detail, crafted his persona perfectly and then... went for John Watson.
I'm talking full-on wooing, pretending to be friends, going on coffee dates together, over months slowly worming his way into Johns heart and mind.
They're the cute happy couple that sits in a restaurant and hold hands, smiling at each other for 2 hours. They watch TV and fall asleep cuddling on the sofa. Pull no punches, because they're ridiculous and sappy and everyone is sick of them because they're so cute.
I like to think it was all about Sherlock in the beginning, but then Jims plans start revolving more and more around his Doctor.

Sooo... what happens then? Was it all just a sick game and Jim betrays John in the worst ways possible? Does Jim try to subtly estrange John from his best friend, "burning the heart" out of Sherlock in quite a different way? Or did John get under his skin, making Jim want to keep up this illusion forever?

(my shipper heart wants a happy end, but I'll leave that up entirely to the author :)