From a developers point of view: If you create a GUI application and follow the rules, you install desktop files (usually in /usr/share/applications, but there are other possibilities) and Debian menu files. It's the developers task to follow certain guide lines when creating the appropriate files and this includes selecting the right category (and perhaps sub-category) for his application. (http://standards.freedesktop.org/menu-spec/latest/
Properly installed applications should appear in the LXDE program menu and the Debian menu respectively.
From a users point if view: If I install a GUI application (from a repository or a properly configured application using dpkg) it should appear in the proper category of the program menu. Everything else is not user friendly.
Some GUI programs are not properly categorized (mostly older ones). The usual workaround was to let them appear in the "other" category. At least a better solution than excluding them from the menu completely.
(I'm not aware, that my program menu was cluttered with things that are not GUI programs at all).
It's the developers task to give his software the right title to appear in the desktop menu. Where do we get, if designers start to rename things as they like? A recent example: Idle and Idle3 have been replaced with Python and Python3. Python(3) is not a GUI application at all, but the default Python editors Idle ad Idle3 are. These editors have the same name on all systems including Windows, MacOS and Linux. When it's good enough for millions of systems and referenced in thousands of documents by that name I cannot see a single reason for renaming them to something else. And if you want to do that, then call it something like "Idle (Python Editor)". But removing the program name from the entry is only misleading.
The latest UI-upgrade has removed lxappearance and obconf from the program menu. Instead of those a new, very simple desktop appearance tool has been added, which is not completely compatible with both.
Lxappearance is an integral part of the LXDE desktop system and it is needed when you want to have fine-grained control of your desktop in many ways. Yes, it's complex and has a lot of possibilities. But that's the price you have to pay for a highly configurable desktop. The same is true for obconf, the configuration utility of the OpenBox window manager.
They are still there, but you have to call them from the command line now, although they are regular GUI applications. This means, that most users will never find them and will never be able to control the desktop GUI in the way it is possible.
This is not restricted to the desktop appearance alone but also affects many GUI programs. All developers of GTK+ software that stick to the rules and let the user theme their applications (icon sets, icon sizes, fonts and font sizes etc) with the desktop tools are fooled. I have described it in my Minimal Kiosk Browser manual, how the user can theme the interface of kweb using these tools, that have now vanished for the normal user.
If Simon thinks, that he should add a simple application to change certain desktop settings, I don't mind, of course. But it should stay compatible with the regular tools and he should not hide those tools from the user.
From a more educational point of view: Configuring a computer (software) is a complex thing and will ever be. Removing that complexity from the user will not help him but cripple his possibilities. And it will give him the wrong impression that things are always simple and that he doesn't have to learn anything. The result is a large number of people using computers that are computer illiterates. I've done a lot of support in my life and know what I'm talking about. You won't believe how often I have been called with questions like: I know that I saved my document and cannot find it again. Where is it? And if I asked for the name of the file and the folder where they stored it I got answers like: what is a folder?