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.
Arc Fatigue: Due to how the battles can take weeks and the comic updates three days a week (Now at random), by the time a battle's finally done, you just want the story arc to be finished already.
Ass Pull: Rocky's "Random Attack". The author has been better about that, either ignoring it completely or simply having it activate as a useless move. With a bonus of adding variety instead of just abusing one strategy over and over again on Rocky when it's not an over-powered move, but not useless either.
Some fans think that the Monty storyline involving his string of curbstompings coupled with unusually long intervals between updates may be the comic's shark-jumping moment.
And in the final part of the storyline, we discover Monty is an ALIEN!
Mind you, the fact that Brendan decided to punch Monty in the face instead of battling him was very well received indeed.
Seasonal Rot: It's not a huge amount, but the quality of the writing has suffered in later arcs.
The Scrappy: All three protagonists have major Scrappy points.
Brendan is a sexist and selfish asshole who is incredibly stupid and treats his friends besides Rocky like shit.
May is a bit of a bitch and set it up so that any money the guys make from trainer battles goes to her and she does nothing but act like a generic Tsundere to Brendan.
Wally is the quirky Jerkass who outside of that and being obsessed with the color green, is a very bland and boring character.
Rocky has some shades of this due to the author's tendencies to make him a Boring Invincible Hero in the earlier story arcs. Nowadays, not so much.
Monty Zuma, but this seems to have been intentional since he's an annoying brat who was dumped years ago by May and still acts like they're a couple and used to harass Professor Birch endlessly. It turns out that he was a cruel bastard who tortured Pokemon.