Yes, Plesk is a mess right now.
For an ideal hosting control panel, the gui should be a stand-alone thing, with a database back-end, all interfacing to absolutely bog-standard distro-supplied rpms for mail, web, etc. Parallels (or rather SWSoft) did lurch in this direction at one point (on Scott's suggestion, if I recall) and things improved massively. But the momentum was lost and they seem to have stopped progress and stuck with propriatary qmail, and non-functioning postfix, and whatever other things that won't let Plesk work with Apache 2.2.
Talking of Apache, I can see that the hard bit is to keep things working when (for example) a new version of apache comes out that uses different config files or commands to an older one. Webmail integration is probably a problem too, as is phpmadmin and so forth, but with a bit of thought surely it can't be too difficult to arrange for everything to work together, especially if you make sure the "configurators" were GPLed and therefore when something new comes out, someone can adjust or even create a configurator that looks at the standard install and config and adjusts it as appropriate.
Webmin is a good example of an OS-independant configuration editor, and there are "hosting control panel" plugins for it. But the gui is quite frankly awful and the facilities limited. The best thing about Plesk (to 8.6 at least) is that the Gui is very good indeed. I'm not so sure about 9.x.
In fact I have to be honest and say that with 9.x Parallels and its insane need to SAAS everything up really seems to have lost the plot. They have already lost literally $1000s of dollars worth of business from my company alone. And while that's not going to make a difference, when you multiply that by all the other companies similar to mine, it all adds up to a very substantial amount. Maybe that's why their QA sucks these days
It is like what Dell is doing at the moment ... the RAID cards they are going to release from now on won't work with normal SATA or SAS drives. ONLY ones you buy from Dell. Essentially a lock in that makes your hardware potentially useless the moment the warranty runs out. Although it might in theory increase Dell's revenues, in practice it is going to put smaller and medium companies off Dell completely, and revenues will decrease. Parallels is kind of doing the same thing by pricing itself out of the small business market (not to mention screwing the product up completely).