The 2d, 2.5d or 3d is honestly up to you - RMXP, the typical engine used for fangames, is 2d based. If you're looking to make a 2.5d/3d project, I would definitely check out another program more suited for that. Long story short, which option for the style of game is based on your experience, and if you have the capabilities to make a 3d game.
I'm definitely a fan of Megas! Z-Moves I'm definitely a bit more iffy on, but they can be good sometimes. Gmax is about the same as Z-Moves. Not a personal fan of fakemon, though it does depend on the designs. If the mons are well designed, and balanced properly, a fakemon game can be a blast.
In the end though, it's your game, so whether or not to include a feature is up to you :)