These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Emily is either a heterosexual girl attracted to Ash but unable to go further in their relationship because Ash is currently a girl OR a lesbian/bisexual in denial who simply doesn't want to accept that she's attracted to another girl. Which interpretation of her character you believe depends upon which side of the shipping war you fall on.
Emily: The only things I know she wants are things I just can't give her...
There is also Rumisiel who is either a textbook alcoholic stoner who needs to be pummelled at every opportunity for being such a massive Jerk Ass loser, or he is a pretty decent guy who has some major self-esteem issues which caused him to take refuge in aforementioned substances and is actually of at least above average intelligence.
There are some that take that former even farther: plenty have noted that he could easily be an Unreliable Narrator about the story behind the misfile, especially in regards to his supervisors. If you take this to a radical extent, it could very easily be that he was flat-out lying when he said the people in charge of the Celestial Bureaucracy would make the changes permanent to cover their own asses; Rather it's really he who is lying to cover his own ass by making the two people that remember the change afraid to let anyone know about it before he can fix it/cover it up himself.
This is probably way off the wall, but God: an omnipotent slacker who passed off his job to the Celestial Bureaucracy, or an active deity going out of his way to set up circumstances to improve the lives of a bunch of humans and help a pair of angels atone for mistakes while fixing up an imperfect filing system prone to a misfile.
Missi: Rich kid so used to getting what she wants she refuses to accept anyone dumping her, or does she genuinely love Ash?
A meta-example proposed on the forums: Is Missi deliberately a character that splits the fanbase?
Angst? What Angst? - Ash angsts constantly about the problems from his-now-her Gender Bender. But he never angsts (or even notices) that his pre-Gender Bender life was much worse; he had no mother, his father was cold to him, he had a grand total of two friends (or, for that matter, people he even talked to), and so on.
Worse is up to debate. He was apparently satisfied with his life. You don't need those things to be pleased with your life you know. Particularly if you're as monomaniacal about something as Ash was about street racing.
You have to keep in mind the intense mental and emotional effect of suddenly becoming the opposite gender and having your entire life and past changed to something you don't even know everything about overnight.
Furthermore, a fair amount of angst is due to the fact that his life is better as a girl.
Okay, but how about Emily? She just lost the last two years of her life. Oh, and all of her former "friends" didn't make the jump back. So, she's isolated, stressed, and confused, and she never complains about it. (Okay, she does, but it's very infrequent and I'm unsure where in the comic it is).
She even says so, which pisses off Ash since he's NOT happy with the change. Then they have a big "I want to help you, but I like my own life" thing, where she probably was about to admit she'd love for Ash to be a boy again, because she wants in his pants, but not as a girl.
And when she finds out she's supposed to be dead if not for the misfile... she doesn't really angst about it.
Rape, or at least an attempt, is very easily brushed off by the female characters.
Anti-Climax Boss: Out of the racers Ash has faced so far, Sheldon seems to have been the easiest to beat. That could just be because of all the lead up though.
Anvilicious: While Chris is usually pretty good about it, there are a few strips that make it more than clear that Ash's character is supposed to be read as a FtM transsexual, and that everything he goes through is supposed to drive home An Aesop about accepting transsexuals, except for the ones that are supposed to drive home An Aesop about accepting homosexuals.
Base Breaker: Missi started off as The Scrappy, but has since evolved into one of these thanks to her positive qualities balancing out her negative ones.
Fanon Discontinuity: Subverted. Despite repeated Word of God to the contrary some readers insist that Ash was only convinced he was once male by the misfile because nothing contradicting this interpretation has ever appeared within the comic itself where it would undermine the fundamental premise underlying the story. Presumably the Word of God will be redeemed at the comic's conclusion but discontinuity cannot exist in the absence of continuity and dramatic integrity sometimes requires an author to leave sufficient room for misinterpretation.
"Funny Aneurysm" Moment: Rumisiel's line from very early on, "Enjoy all the extra time you've got", takes on a whole new meaning once you learn that without the misfile, Emily would be DEAD.
Game Breaker: Ash's Monster XR, which is so wickedly over-the-top for a high school street racer that it must remain parked, lest it suck all of the dramatic tension out of the storyline and threaten her underdog status.
Harsher in Hindsight: In this strip, after Emily's mother tried to persuade Emily that she shan't associate with Ash because he (or rather "she", from Emily's mother's perspective) was sleeping around (having overheard parts of Emily's earlier conversation with Ash) with other men, Emily replied that Ash only did it once and was so off-put by it "she" wanted to never let another man touch her, and her mother voiced her concern about whether Ash's experience was rape and if she was okay. Just a moment of awesomeness for Emily for being able to put her overbearing mother down, right? Except not, as the story progresses further it becomes apparent that the misfile did leave Ash feeling violated and scared, and it is very likely that at that moment he really felt raped.
Hollywood Homely: Missi is supposed to be flat-chested. Of course if it were drawn too subtly, you couldn't see her breasts at all… which is apparently not the point. She wears padded bras most of the time.
Memetic Badass: Doris became popular on the forums after her first (and at the time of this writing, only) appearance.
Many fans can't understand why Ash would ever want to be male again.
A bit of point-missing from the creator - a recent story looked like it would finally resolve the Ash and Emily romance when it the subject was suddenly dropped and the scene changed. The fans got enraged at how poorly this scene was resolved and how stagnant the series was becoming, so Chris decided to write a post commenting that... we shouldn't be so upset that Ash and Emily didn't get together in that moment.
Despite the protagonist being male inside a female body and numerous filler specials pointing this out, along with Word of God, many readers insist Ash is a strong female character.
Moe: Ash, especially with Missi being Ash's girlfriend. For that matter, Missi herself.
OT 3: The series is now having Ash, Emily, and Missi hanging together so much that this has begun to enter the minds of several followers.
Unpopular Popular Character: Many fans feel that Rumisiel gets too much crap from the cast. Which is ironic, because the guy himself believes he deserves it - the flaws his brother and Dr. Upton point out are quite evidently there. More importantly, it's Ash and Emily who gave him the most crap because he upturned their lives (especially Ash, who's understandably having an identity crisis thanks to the misfile). Additionally, later books have shown Ash and Rumisiel are reaching a kind of understanding, anyway.
Wangst: Much of the comic finely treads the line, but so far it hasn't really stepped over.
The Woobie: Rumisiel and Ash take turns; Emily, when she's fighting with her mother. Aiden to some. And Missi has recently had even the haters wanting a plushie to hug and comfort.