First off, as previously stated, why fix what isn't broken? The menu system just works, and it actually streamlines gameplay, in this instance. Additionally, simplicity is the name of the game when it comes to Pokémon. Why else would the DS games have 3D buildings but maintain a constant camera angle similar to the one in the Gameboy games?
Second off, the amount of work involved is a bit too great for some developers. Some people are either unable or unwilling to put in the effort to develop a mouse input system. The difficulty of it is either too great or too time consuming to some people. And in case you haven't noticed, many developers here are still in high school.
Third off, and this is just my opinion, people seem to want to create the console-style RPG feel. If we wanted to make a computer-style RPG like Ultima or Doom, we would. While yes, RPG Maker XP/RGSS is the typical platform combination used, it's used because it creates this feel both easily and completely (when the Starter Kit is added to it).
But really, in all honesty, if the developer wants to change the menu system, he/she will. It's up to them, and if they want to try something different, well, all the power to them. If the menu system works well, then, there you go. If not, whatever. If the game is good, you will probably play it regardless of the menu system (unless it is completely broken, of course).
Oh, and about the graphics thing, speaking as a graphics artist, creating larger sprites in the Pokémon style that aren't boring is quite a difficult feat. I was developing a tileset that utilized RPG Maker XP's default resolution, and I think the only graphic that actually looked decent was the water. Pokémon, well, they are already pretty basic and respriting them to be bigger isn't as difficult, especially with Sugimori art at your disposal.