1. I don't blame the skinners for not making any Messenger Plus! skins, as it requires a lot of time, and most standard users doesn't care about it (but I do). I also think that this is the reason why no Messenger Plus! skins has been submitted or made.
But if they were split up, they could easily get a lot more attention, and users that actually want Messenger Plus! skinned can get it skinned.
It's true that Plus! has always supported custom skins through the Interfaces-directory, but not like this. And if those skins would install files into there, we're back to dodgy .exe installers, aren't we?
2. It's the "features or security" question. You say it can give Plus! a bad reputation, but it can also get a better reputation if such nice per-pixel skins were possible. All skin-scripts should be tested (by you MenthiX!
), therefore no official skins would include malicious code. If you install it from a unofficial source
3. New request on the skin-script subject! Do a encrypted signature on every skin verified, and then if there isn't a signature or if it doesn't match, it would give a "this may be malicious code" warning. There's no way to fake that signature without the key, and that key shouldn't be stored in Plus! so it's not possible to extract it. Therefore verified skins should be able to install, but non-verified skins will give a warning. Bruteforcing would take about 1000 years, simply not worth to try.
4. Another new request on the skin-script subject! Use a stripped-down version of the scripting API, giving the skin-scripts only access to functions which would be necessary when making skin related stuff and settings-dialogs.