My point is that after the initial investment in the setup, it takes almost no time to maintain them. In my particular case, I invested about 2 weeks tweaking settings here and there until I felt comfortable with it. After that initial setup, it just gets out of your way.
Personally, my biggest issue is getting vim to work the same way on multiple platforms. I have a mac at work and alternate between windows and linux at home. Each of those has been slightly different than the others. To some extent, yes, once you have the config set you can just leave it alone and be fine. But for me, switching to a full IDE has made life easier.
I'm really intrigued by what all you're doing that you have this kind of problem. I maintain a pretty complex vimrc, and deploying it is normally just a git clone. I've never had any of these issues, and when I started at google (which provides a nice collection of internal vim configs and plugins), combining the two and getting everything set up took me O(hours), not O(days). What are you doing?
I simply updated mvim and :E stopped working on OSX.
I could work around with NERDtree, but its one of those things turned into a timesink when I didn't need it.
Have you considered that your usage is at fault as opposed to vim? Out of 127 plugins installed and even more tried I cannot recall ever having an issue other than having bound a key that the new plugin would have bound.