Speaking completely for myself only, I'm very happy to not have the menus there. It's so much nicer to find the library item I want to watch in Plex and then have it actually just immediately play when I select it rather than have to then go through another annoying DVD menu. As for commentary, I simply include the commentary audio track when I rip the movie (in the same way I can include multiple language tracks). I similarly can include a subtitle track if I want to, though when ripping from DVD those subtitles are going to be in VOBSUB format, which itself isn't currently compatible with streaming (so I can just go find a SRT file for that, which will work fine).
The only thing I'd miss would possibly be the "extra" features. But you know what? I very rarely bother watching them anyway. And if I want to do so, then I can go pop in the actual DVD, since I'm ripping from my own personal DVD copy, after all. And eventually, I figure Plex will also probably support the ability to associate "related" files to a library item (trailers, extras, behind the scenes, etc.), so when that happens they can be ripped individually and included in the library, too.
And, finally, if I did use VIDEO_TS or some other disc image format, I wouldn't be able to watch the content remotely on my Android phone, on my iPod Touch, remotely on another desktop client via myPlex, or to share content with friends via myPlex if I choose to do so. Disc image formats basically lock you into a local desktop client and that just restricts all the power of Plex! =)