If I run aMule on a server, the GUI doesn't work very well (at least amuleGUI).
When I browse files there, I can see that I browse local filesystem, not the remote one where the amule instance is actually running.
So I got quite suspicious regarding usage of GUI 
While it's still far from perfect, setting the configuration should mostly work. File browsing is probably simply not implemented. You mean for setting up the shares?
Yes, shares and cathegories.
Regarding the remote management, I don't really know what works and what does not. I once wanted to set up cathegories remotely and when I have discovered that the browsing stuff does not work, I gave up. Checking what setting works and what does not can actually be quite tedious. For example I have not found the "try to download first and last chunks first" option in the config file. Therefore I think that I can't reliably tell whether it has been applied or not.
Since we have nettops here that can serve as routers or low cost servers, I think that more people will consider running amule as a daemon, so it would not be bad to make it somehow easier for them, that's what I think and what is behind my suggestion...
Agreed, but I'd rather make it easier for them by improving the remote gui than by forcing them to edit the config and improve that.
Well, AFAIK Linux users really love editing config files. Maybe others could, too. If you want to change aMule preferences remotely, you would probably prefer using ssh and then editing a (commented) config file. If you have an idea how is the thing you want to edit called, you just search for that option with an editor and you are done much faster than searching for in a menu and you know what is going on, you have control over things. Anyway, I don't want to force users to edit files if they don't like doing so, it's just about another approach.
And you don't have to have aMule installed to do this. Installing aMuleGUI just to be able to change amule settings is an overkill, isn't it? Well, at least for users who are familiar ssh

Usually you get aMuleGUI only in a package bundled with aMule, moreover you have to satisfy dependencies, which can not be always possible.
The statistics (total upload, total download) are saved with the config.
Doesn't it sound strange anyway? Saving stats to config file?
You can have another file that is periodically updated, and it could contain internal statistics data, but maybe also a general transfers status - and you could peek on how are downloads going without having to use aMuleGUI at all. Maybe not usable for most users, but quite nice for people who like playing with things

Oh yes, and one thing more - since we have SSDs here, maybe the save interval of that file whatever file it is, should be adjustable. Since SSDs don't like rewrites, some users could prefer longer save periods.