On the wiki, I've been advocating the use of a seperate mod directory (/multimissions, as it happens). In my opinion, nothing should go in the root directory except for scp builds. Keeps it neat.
While I agree with you in principle the multi missions and the cutscenes are both perfectly valid for root. The cutscenes are a replacement for the mve ones so they're fine.
As for the multiplayer missions they're installed to root by Turey's installer and I'd much rather see everyone standardise around that than having everyone recommend different places to put them.
Besides if you place them in /multimissions you lose the ability to choose whether to run them with the media VPs or not with a single selection in the launcher. For the same functionality you'd need to add a second /MultimissionsVPd folder or some such or add a mod.ini to the media VPs folder pointing to /multimissions.
It's much easier for all concerned to just stick them in root.