Unresolved plotpoint, true.>shapeshifter,
That go resolved just fine. Although his comments about the author were CLEARLY referring to Biddleford and not Stanford, which makes no fucking sense, and seems to imply that some of the plot, even as late as season 2 was undergoing heavy revisions.>the purpose of the alien ship in DaMvtF (unless it was just telling us how the shapeshifter got there)
Really the only thing unresolved about the spaceship are if the ship caused the GF centered weirdness, or if GF weirdness was why it crashed there, and coded comments about "The Probability Drive" strongly imply the former.>why there was a cult of people erasing their minds,
Because McGucket formed a group to help people who had seen and couldn't handle GF weirdness. Except over the years they went mad with power. Probably due to Blind Ivan's influence.>if there was any special reason why Blind Ivan was part of Bill's car
Probably just a shout-out or reference.>why Bill wanted the journals destroyed /before/ the portal opened..
A massive plot hole for sure. He wouldn't have known about the secret invisible messeges, so surely he would WANT all of the books found so they could finish the portal and open it. There was literally NO reason why he would want them destroyed.
Here's some other plot holes>Was there anything up with how a LOT of cast members were missing parents and nobody ever addresses it?
Wendy's Mom, as mentioned Biddlefords Wife, the Mabel and Dippers parents, the whole Shermie conumdrum. Hell the ONLY missing parent issue that is ever addressed is Soos's.