All of the work being put into Prism, especially all the mechanics imported from future generations. Abilities are in there, and cries of Pokemon as late as Generation VI are imported with accuracy beyond what was expected from the Game Boy Color's sound capabilities. Full character creation was also implemented, with front and back sprites and adjustable outfits and colors. Most amazingly however, after the leak of Prism it was discovered that the Prism file amounted to a mere 2MB, meaning that even with all the additions and added sound files, the game was still roughly the size of Crystal memory-wise and thus could run on a physical Game Boy Color cart without issue (as proven by multiple fans within hours of the leak).
The leak of Pokémon Prism mere days after its cease-and-desist-ordered cancelation caused great excitement and virtual Hail-Mary's amongst fans on 4chan's /v/ and /vp/ boards and the Prism subreddit on Reddit.
The Fakemon Legendaries in Prism. People either think they're well above usual Fakemon standards as far as hacks go and don't look too far off from regular Pokemon, or they get accusations of falling into the same cliches Fakemon use and/or don't look like Pokemon to begin with.
Earlier, the same criticisms were made about the now-scrapped Prismeon, which would have been KoolBoyMan's original contribution to the ever-popularEeveelutions. The Walking Spoiler nature of this Pokemon also magnified the fans' reaction to it when they found out about it. Eventually, it was scrapped sometime before the aforementioned Legendaries.
The third gym leader of Prism, Brooklyn. She has only three Pokemon, one of which is a pre-evolution of the other, and all of which the player has faced earlier in the game.
The sixth gym leader of Prism, Ayana. Like Brooklyn, three of her four Pokémon are ones the player has already encountered, two of which are used by her own trainers. Furthermore, because of their weakness to Fire-type moves, a faster Fire-type Pokémon could sweep all three of them. This isn't so much of the case of her wild card: Drapion, a Lightning Bruiser which doesnt have a weakness to Fire, and in fact can use Earthquake to counter them.
While the quality of Brown had few doubting that Prism would be a solid production, the sheer scope of the changes and the vast amount of new features Prism packed in resulted in thoroughly-impressed adulations from players after the leak.
That One Boss: Fighting-type gym leader Andre comes at the end of a tough segment of the game, and uses a well-rounded team that covers the typing's weaknesses and capitalizes on its strengths. Three of his four Pokemon - Gallade, Lucario, and especially Machamp - are top-tier threats that will be a nightmare to unprepared players. Thankfully, he doesn't appear in the final Naljo gym's Boss Rush (probably because his anti-civilization outlook wouldn't allow for it).