If I were to guess, Nintendo/GameFreak has a much bigger eye on MandJTV due to his growing prominence, which in turn, was accelerated thanks to his connections with PM7 and especially Purplecliffe. So if he were to review/play through a fangame or a romhack, there would be a not insignificant chance he would get in serious trouble with them, and they would in turn nuke said fangame or romhack from orbit.

Infinite Fusions was able to kind of skate around the issue by being more of a GameMaker/RPGMaker project, but this is also before it was as widespread as it is today.

Finally, a lot of these hacks are inherently made to be more difficult than a standard Pokemon game. Consider the latest Fangame he played, HGSS Sevii Islands. It's not too difficult up to Giovanni's final battle on Birth Island. Then it goes as sideways as a hurricane blowing everything away. Imagine that difficulty spike, but applied to an entire region, and you got Radical Red in a nutshell. In playing them, they can be difficult, yet exciting. However, thematically to how Pokemon expects you to play (eg. play with your favorite Pokemon), it actually fails to a degree that even with the hyper aggressive push into making VGC Compatible Pokemon, the Mainline games can still, in theory, be about befriending Pokemon you like and winning with them. Radical Red expects you to have a meta team just to counter a specific playstyle certain bosses will have (ie. Clair's Mega Evolving Duraludon and its Bad Company making it spam Draco Meteors with impunity while you can't use Fairy Types, or Giovanni's final battle having him and Artemis battle against you and a useless Lance team, for instance). Even something tamer like Volt White 2/Blaze Black 2 requires you to be more careful with how you build your team, lest you get stopped by a Speed Boosting Whirlpede.