@Shaz - Indeed, default RM Games do lack the ability to automatically apply updates into a game. There are scripts available though that can be used to implement a manual patching system - such as the patch script by yami, and then there is the one I done also.
But yea, either way it is something that one would have to implement themselves, at least in some way - such as adding scripts.
Additionally, with that kind of system, the players would have to keep up-to-date with the latest version and manually download/install each new update.
@Andar - Close, but not quite...
1) Yes, you are right in saying that you need to be connected to the internet and also have a means of storing the data intended to be downloaded; however, this does not need to be a 'database' of any kind. Additionally, it does not need to be an FTP process.
Additionally, you say that you can not use "some simple file storage site" - I assume you mean something such as dropbox? Again, thats not right - using such a thing is completely possible if you know how. Hell, using pastebin / github / dropbox / a website you own - its all the same crap at the end of the day - 'crap' being the transmission of information over the internet.
2) Yea, it certainly is not an easy thing to do, and there are limitations that must be obeyed; however, not as many as you may think. For example, any $game_object's data can be overwritten / updated, such as $game_actors[1]'s name, or image, or notebox, or whatever. Any script class / module / line of code can be modified / altered / overwritten. And maybe best of all - rvdata2 files can be altered / overwritten (wouldnt recommended deleting anything other than a map.rvdata2 file).
Furthermore, You can 'remove' content from the game - most of it anyway. The only real things that you cannot remove or alter are the files that require processing constantly when the game is running - this being the Game.exe and RGSS301.dll.
Also - you could remove the rvdata2 files completely - such as a Map002.rvata2 file (or whatever) - just have to make sure that nothing in game attempts to trigger the file. This kind of thing though is something to be vary wary of as it would obviously cause issues if you where to try and remove things like the scripts file or whatever.
3) Again, there is no need for a full database, but yea, you are right in saying it would require someone to write the relevant system to process everything correctly.
@gameofthedungeons - I am actually almost finished a system that does exactly this. - I say 'almost finished', still have to finish and then document the system, write a pdf, get a beta tester or two, fix any issues, add any suggested features and whatever else crops up - so yea..
As Andar stated though, if this is your first RM project - give up the idea and keep it in mind for a project in the future - after you have gained sufficient knowlege of actually using the RM engine. The reason for this is because its not an easy thing to do - and if you are trying to code everything yourself its going to take a LOT of time learning / facepalm-ing / headdesk-ing / crying / curling up in the shower / and most of all, making lots of mistakes.