Well, actually most of your issues can be fixed :) Yes they don't do the job for 100%, since as you said it doesn't understand your code, but it can come pretty close
Python - vimpy Java - JavaImp JS - ImportJS
Syntastic or YouCompleteMe
I've heard about clighter8, which can do some refactoring for C/C++, haven't checked myself though
The goto command in YouCompleteMe
goto
YouCompleteMe
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Well, actually most of your issues can be fixed :) Yes they don't do the job for 100%, since as you said it doesn't understand your code, but it can come pretty close
Auto import
Python - vimpy
Java - JavaImp
JS - ImportJS
Syntax check
Syntastic or
YouCompleteMe
Refactoring
I've heard about clighter8, which can do some refactoring for C/C++, haven't checked myself though
Navigation
The
gotocommand in YouCompleteMeType based autocomplete
YouCompleteMe