Uhm how about this?
Atmosphere and Weather Generator Version 2
> Since they already started building rain, storm and snow, why not they expand to something like Sandstorm, Spring, Summer or Fall? That way, there would be a good blend of atmosphere or feel of the game map. This could also be adjusted, so the developer can adjust the time and duration of these to happen. Much like its a weather, it can also be a good feel for the game maps.
Extended Resources and Characters
> This may have been mentioned, but perhaps expanding the resources for Ancient, Golden Age, Modern Age resources would be good. Although it would surely be the Ancient - Golden Times as the concentration of an RPG game, some developers would likely want to make a modern based RPG. Maybe enterbrain could provide us a bit more usable characters and all the other stuff so we can suit our game's graphics better.
Editable Graphical Menu System
> This would probably the one I really wanted RPG Maker has to have in the future. Perhaps we can edit a bit of the Menu System like make it scroll smoother or scroll with actions like the menu of Wolf RPG or Battle Realms, something like that. This would probably be hard and tiring for the developers to make, but hey, its just my suggestion.
Extended Battle Characters
> The "4 Players" rule in battle is kinda old and what if they make something more than that? Perhaps they could change it to 4-7 or 4-8. If you notice, Troops can handle a maximum of 7 units, either the same enemies or of different enemies. It seems unfair to battle 7 enemies specially if they are strong when your party is just 4. Although I know there's no game maker who would actually create a troop just like I mentioned, its just again my suggestion.
Connectivity Chat System / Mini Chat Connection System
> I saw a dll / script from White Flute and Tomoaky wherein, they were able to get NND (Nico Nico Douga) placed inside RPG Maker. If this is possible, there's also a possibility that perhaps they can let game makers create a certain chat site (chatango?) or any relatively chatting site, so players can connect with each other and chat on the game. This is not the MMO thing, but rather just chat system. Of course this is a ridiculous idea since someone might say... "Why not chat in chatango while playing the game?". Well, perhaps playing the game and chatting is much more enjoyable than shifting window to window or something like that.
Debugger / Debugging Tools
> Maybe a tool for debugging. A better one.
Artificial Intelligence System
> Perhaps they could create or let us makers generate an AI for enemies or characters on MAP, suitable for Action Battle Systems.
Patching System
> Some games, say for example are updated maybe a week or a month with improved features. Aside from recompiling / recompressing the game files, take the Game.rgss3a and upload it, maybe a graphical patching system embedded in the game tool would be nice.
These are just my suggestions I thought of. I know some of you might hate it though xD