Subtrees interact with history in a much more obvious, configurable, and automatic way. The most obvious win is never having to run `git submodule update`. The better control over history is the bigger, but less obvious win. Since you have some experience using submodules for your .vim, maybe try switching to subtrees and see what you think. I like the Atlassian blog post[0] about them for getting started.
For me the the most obvious win is still being able to merge, move forward in time, move backward in time, rebase, etc. Everything that makes Git great.
Once you have submodules in your repo, all that becomes heinous. PLUS everything you mentioned...
Sure, if you don't use those features, then submodules would probably work fine. But then why not just use Dropbox?
[0]: http://blogs.atlassian.com/2013/05/alternatives-to-git-submo...