It seems like the delay in knowing that Stevie made it to NYC really changed the focus of/derailed the investigation early on. Between all the bureaucratic wrangling about where a MP report could be filed and the over-focus on the road trip (in my opinion; given that it is now known that she got back to NYC safely, alone and at basically the time she told her mother she would, it seems unlikely this has anything to do with her disappearance), resources weren't poured into investigating/looking at the correct area until way too long after the fact.
Watching the Find Our Missing video and reading the comments on various websites/blogs, it seems like most of those close to Stevie believe the BF (BK) knows more than he's telling. This seems to be the most likely explanation to me as well. If Stevie kept in touch with her mother during the whole road trip / told her truthfully exactly when she was getting back / etc, there's really no reason to think that she randomly made up the story about going to pick up her stuff from BK's... That would, after all, be a natural thing to do post-returning to NYC and not something her mom would want her to do for any particular reason (i.e., there's no reason she would make up the story to make her mom feel better).
(It strikes me as particularly plausible that Stevie would head to BK's to pick up her stuff upon return if Stevie and BK broke up a little closer to her road trip than the FOM video would lead you to believe (no exact date is given)... There is some support for this theory in a back-and-forth on BK's FB, where he indicates he is sad that he is single -- and Stevie replies -- only a week or so before she goes missing.)
Given that BK told Stevie's mother that he never saw her at all, you have to think: (1) she lied to her mom/changed her mind about where she was going (obviously, possible... but why?); (2) BK had something to do with her disappearance; or (3) something happened to her between PA and BK's... at 9 am in busy areas of Manhattan/Brooklyn and no one saw anything (seems unlikely, in my mind). Option 2 seems by far the most likely to my mind.
Now that the skeleton has turned up, I'm curious if the fire at the house happened at around the time/just after the police finally interviewed BK. Possibly he had her body in his apartment and ditched it when he was worried police might get a warrant. I'm also curious about substance abuse. Many of the changes to Stevie's personality that are described seem potentially consistent with substance abuse... There was also a lot of substance abuse around the OWS crowd. (BK also appears to have lost a lot of weight in that time period based on online photos available on social networking sites in a way that seems consistent with substance abuse.) If Stevie was using, that could be another way that she could have died that BK possibly would have covered up.