I came across this decision some weeks ago.
I chose Rom hacking.
Why? Because as an aspiring game dev myself, one of the main reasons I wanted to craft a Pokémon fangame in the first place was to practice on many aspects of design, such as pixel art, game mechanics edits, and my writing. A rom has already a working engine and a game for you to tinker with, to carry your material, as well as a good load of easy to use tools at your disposal to implement them.
Another reason would be that if I wanted to spend the effort to learn and code a game, I'd rather just make it an original work instead. When it comes to Pokémon, it's much less work to do- you are just editing from the game to your liking instead of making something from the ground up, and that lends itself well as a practice run, where you go for exactly what you want.
What else. Right. Limitations don't necessarily mean a negative, especially for a pixel artist. On the other hand, it somewhat forces you to be creative with what you can do, and narrow your focus to it. Usually for efficient and fast results.
Edit: OMG how could I forget the best part of this. Haha.
As a GBA rom hack, I can play it on my Game Boy Micro. Heh. This alone makes it all worth it.