When Stan told Wendy and Soos that he'd "fire both of them if he could", did he mean he'd be unable to find other employees, or that he'd be all alone if they left?
Both the twins have this in spades. Is Dipper a good-natured, intelligent kid who only seeks for the truth regarding the journals or is he a dangerously obsessive child who wants to experiment with a hazardous book and encourages Mabel to make decisions they know are immoral? Is Mabel a fun and All-Loving Hero who lightens up the mood or a continuously Innocently Insensitive and self-absorbed brat who takes advantage of her brother, never learns her lessons and whose flaws are rarely spoken of and poorly addressed?
In The Inconveniencing Mabel knows exactly what the Smile Dip is, and that it's banned in the US. She also has no freak-out moment when dealing with its...effects. There are quite a few scenes that make more sense if you assume that's not the only time in the series she's high.
Did Robbie really not know about the brainwashing subliminal messages in the song from "Boyz Crazy" or was he lying to save his own ass?
Even with his official revelation, Bill Cipher still remains the subject of several conflicting interpretations, due to the nature of his mysterious end goal. There's divide between those who think he's "evil" or simply Chaotic Neutral. As of The Sock Opera, Bill seems to be leaning more towards the evil side, as he tricked Dipper into letting him invade his body, then destroyed the laptop from the bunker before Dipper could pull anything off of it, physically abused Dipper's body simply because he had forgotten what the sensation of pain felt like, and then nearly tricked Mabel into giving him Journal 3 so he could destroy it and keep the Twins from discovering any more about what the town is hiding. However, depending on what exactly he's trying to keep Dipper and Mabel from interfering with there may still be an argument for him falling under Chaotic Neutral or possibly even Blue and Orange Morality. The latter is actually highly suggested by canon supplementary material.
While we all know he's a malicious Trickster God whose antics would get him kicked out of the Greek or Viking pantheon. Weirdmageddon shows that his home dimension is slowly dying along with all of his friends. Evil friends who eat children and mutate people faster than radiation in Fallout, yes. But conquering a new home and having a party to celebrate seems like a pretty human motivation.
Weirdmageddon Part 3 adds to this when Bill meets with Ford and talks about how he "liberated" his home world which was full of "flat dreams" and now he wants to do the same for Earth by spreading his weirdness worldwide. Is he just trying to swindle Ford again, or does he actually believe that what he's doing will create a better place for everyone since they will be free? For a given definition of free, anyway.
.GIFfany. Is she just a verbally abusive ex-girlfriend archetype who murdered someone in cold blood in her backstory, or is she a very lonely character with deep-seeded abandonment issues who's downward spiral into madness started when her programmer, who may have possibly been either a parental-figure to her or someone she fell in love with, tried to delete her and she was forced to kill them in self-defense?
Wendy arguably has one, as some fans have questioned whether or not she secretly has a crush on Dipper. Granted many of these fans happen to be Wendip shippers since these theories died down sometime after the season 2 episode "Into the Bunker", where she reveals to know about his crush on her and proceeded to gently turn him down. However, these theories regained a bit of traction in the series finale after the two traded hats with each other.
Pacifica is trained like a dog to always put on a good public image, and the whole town seems to like her family. That is, everyone save Candy, Grenda, Dipper and Mabel, whom until Northwest Mansion Mystery she went out of her way to bully. Was she a stereotypical Alpha Bitch having fun? Or was she internalizing the abuse and taking it out on the village idiots? Or was she actually jealous of them for not having as much pressure put on them compared to her and able to live like normal kids?
Ford. It's hard to tell if he's a petty Jerkass who held a pathetic grudge against his brother for years, or if he actually grew out of that grudge and is only mad because Stan risked the universe and billions of lives just for him.
Episodes after "A Tale of Two Stans" seem to be leaning towards the latter, as Stanford actually doesn't seem particularly antagonistic towards Stan once things settle down. The main antagonistic thing he did was ask for his home and name back, which... isn't really that wrong of him, to be honest. The problems in their relationship seem to stem more from Poor Communication Kills than anything else, as Ford doesn't seem to know Stanley lived in poverty and Stanley doesn't know about Ford's work or the full repercussions of opening the Portal.
"Dipper and Mabel Vs. The Future" gives us another part of his personality to interpret. Most of the fandom seems to have taken Ford's speech to Dipper as disparaging Mabel and/or projecting his own feelings about Stan onto her, but he could just as easily be seen as merely recognizing Dipper as the ambitious person he's always been and showing concern for the kids' (and particularly, Dipper's, who has always put his goals and dreams secondary to Mabel's) development as individuals rather than just two halves of a pair (something he seems to feel was sorely lacking in his own upbringing), and that this - always being grouped together with Stan, even at the cost of his own wants and needs- is what he's describing as "suffocating", rather than Mabel (or even Stan) as a person. After all, he does remark on Mabel's own gifts as a person and doesn't think she should be dependent on Dipper any more than he should be dependent on her.
Did Stanley's memory actually return at the end of Weirdmageddon Part 3, or is he simply playing along for the sake of his family and friends? Bear in mind that the first two things he remembered were Waddles and Soos' names, both of which would have been mentioned early on in the scrapbook. He's a natural conman so it's in his nature, and it wouldn't really be that hard to convince them since they already wanted to believe that his memories would come back... On the other hand we have seen an example of memories returning after a memory gun-wipe on the show before.
Worse yet, what if the "Stan" at the end of the series isn't Stan at all? What if it's Bill pretending to be Stan? The memory gun was set to only erase memories of "Stanley Pines", not Bill. While the audience was led to believe that erasing Stan's mind would erase Bill in the process, the memory ray could just as easily erase all of Stan's memories and leave Bill intact. Then all it takes is playing along with the amnesiac act for Bill to get a permanent physical body in the human world.
Fan interpretations such as this bring to question whether Filbrick Pines was truly a greedy, inconsiderate, heartless bastard, or if disowning Stanley was a spur-on-the-moment decision he'd later come to regret.