I had a feeling Bob was the bad guy all along and he was just throwing the shadow of suspicion onto Alex to further his agenda. Plus, Alex and Fluttershy make such an adorable couple. That being said, I'm not all that happy with how he nearly strangled Rainbow Dash with a tree. That made be suspect him for a bit.
I couldn't help but lose a little interest in this comic when Bob just suddenly backstabbed everyone there, he pretty much exposed himself in front of everyone including Celestia, rather than wait for a good opportunity to do it.
I thought the big bad antagonist was suppose to be smart.