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.
YMMV: Pokemon Rise Of The Rockets
Arc Fatigue: The Manaphy Arc, as a result of poor management, excessively common periods of downtime meant for character development that were all clumped together, and constant player punches, all ending in a much-bemoaned Anti-Climax.
Big Lipped Alligator Moment: The entire sequence involving Jake Soren and Jason Alco traversing through a parallel dimension inhabited by "the Entities," massive creatures representing different elements. Their inclusion to the story contributed virtually nothing to the game and has never been expanded upon, and Parugi has since declared it non-canon.
Designated Villain: Team Rocket, primarily due to how forceful their takeover was implied to be and because of the public disturbances that their Mooks have caused. Contrary to popular belief, however, Team Rocket's reign has had a fair number of positive effects on the Kanto regions, and the Shadow Admins have made a point of stopping the trouble caused by their lower-ranking group members.
Moral Event Horizon: Shadow Admin Ace authorizing the reactivation of the Shadow Pokemon project, effectively allowing a group of scientists to perform unspeakable experiments on Pokemon to turn them into super soldiers.
Sabrina has one after killing Archie when she takes his Pokémon, still inside of their Pokéballs, and psychically crushes them, killing all of them as a result. It has since been revealed, however, that she has been under Mind Control by Rocket Executive Elton for some time, along with Surge and Koga, and so this may not have been of her own free will.
Both Ace and Bluefalcon. Two highly-ranked female members of their respective teams with pre-established facts and actions that could have led to some very interesting character development, both killed off rather lacklusterly early on in the story. Parugi himself cites the early deaths of these two (particularly the latter) as deep regrets.
They Wasted a Perfectly Good Plot: Again, the Manaphy Arc is the one that immediately comes to mind, for good reason. Despite the amount of investment that was put into it, poor execution on the part of its managing member resulted in virtually no payoff and much backlash from the players involved.