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.
Angst? What Angst?: The Cutie Mark Crusaders don't seem to think being fillynapped by a monstrous Queen is a big deal. Also Fluttershy is gleefully fascinated by two creatures fighting over the right to eat her and her friends.
Base Breaker: Luna in the second arc. Many really don't like how her character has been derailed back to season 1 "woobie waifu" version.
The existence of the Nightmare Forces for some, who prefer the idea of Nightmare Moon being a corrupted Luna rather than a different entity possessing her.
It IS implied that the Nightmare Forces actually need consent to possess somepony, meaning Luna would have still been in the wrong, but it's presented as a very minor plot point and rather flimsy at that.
The quality of the comic; some people who are angry about Twilight becoming an alicorn cling to the comics as being free of that (until its eventual incorporation in #13, and even then she remains grounded for the entire comic), while others describe them as poorly written fanfiction. Numerous out of character moments, a different tone from the show, and the extremely heavy-handed references (both to the fandom and other media) don't help matters.
Evil Is Cool: Bronies seem to really like the idea of Rarity going evil given all the fanart of Nightmare Moon II has gotten.
Evil Is Sexy: Nightmare Rarity, as nicely detailed here (major spoilers, of course).
This was even lampshaded in the comic when Nightmarity says at one point, "I'm so hot, I should be on fire!"
Fridge Brilliance: One of the trophies the Luna/Big Mac pair win is "Synchronized Water Polo". Polo - as applied to ponies - would be a rather apt sport (and shown true in issue #11), and horses are actually good swimmers so would take well in the water.
In the Sunset Shimmer short, she's seen rejecting the invitations of five unicorn mares: Moondancer, Lemon Hearts, Lyra, Minuette, and Twinkleshine. Now, considering that Celestia was trying to groom Sunset in the same way as Twilight Sparkle later, in hopes she would become a Princess, this would have also likely involved her having friends to become the Bearer of the Elements, and from this, there's a strong correlation in these five mares: Moondancer (Fluttershy), Lemon Hearts (Applejack), Lyra (Pinkie Pie), Minuette (Rainbow Dash), and Twinkleshine (Rarity), even with the brief characterization thrown in the comic.
Fridge Horror: Luna's plan to get Spike and the Mane 6 sans Rarity to the moon is rife with this. Namely the whole "Move the moon closer" thing.note the tides are dependent on the state and orbit of the moon.
Gateway Series: There have been reports of people - not just bronies - getting into comics period thanks to this series. The first issue was one of top 100 best selling comics in 2012. An all-ages comic doing this is good news for the industry!
The fandom has had a knack for publishing fanart of Rarity battling giant crabs. The cliffhanger to #13 has the Mane Six being attacked by a giant crab, and Rarity in particular seems to be really panicky about it.
There was also an Ask Blog about Pirate Rainbow Dash. Guess which canon pony is the most eager to get her sea legs?
In chapter #7, Applejack and Rainbow dash wished that Daring Do was there to rescue them and the others from jail. In season 4, Daring Doo is revealed to be real and Rainbow Dash rescues her.
In issue 17, Celestia and Starswirl travelled to an alternate universe where Dinosaurus still roam and they encountered Fluttershy Tyrannosaurus Rex counterpart, [http://fav.me/d65mwj9 this fan comic] was made a year before issue 17 was released
Memetic Mutation: Several haven become part of the fandom's image macro core image set:
Fluttershy's "Nature is so fascinating" line from Issue #3 has picked up a lot of millage. The circular panel with her has been also used to create "Bad Advice Fluttershy" macros.
Pinkie's reaction to opening the door with the giant eyeball in #4 (replacing the eyeball with anything else)
Rainbow Dash's "Two Words!" at the end of #5
Several reaction shots from the arc of #11-12, including "Cadance laughing at your misery", "Cadance tearing up", "Cadance slyly contemplating", and "Shining trying to say 'Hello'".
Ugly Cute: Jim the Cave Troll. Sure he's a hulking brute who could easily crush a pony if he wanted to, but he's so innocent and carefree it's hard not to see him as anything other than the softie he really is. And he genuinely did love the Mane Six's company.
The uncorrupted moon bunny in Issue #7. Fluttershy certainly thinks so.
Unfortunate Implications: Shining Armor singing a parody of Oingo Boingo's "Little Girls", a song about an adult attraction to teenage girls. Thankfully the comic uses the word "mares" instead of "fillies".
What Do You Mean, It's for Kids?: Its promoted as an all-ages comic, though the series thus far has been a little darker than one would expect from a series where most of the covers feature cute, colorful ponies.
Rarity is very sympathetic in the Nightmares arc, especially when it's revealed that she has self-esteem issues because she fears that her friends will abandon her because they find her useless. Fortunately, her friends convinced her otherwise at the end.
Spike during Nightmare Rarity's dream sequence at the end of #7.
Princess Celestia, as a result of the Sunset Shimmer short.