There is an old well-known issue with WordPress and permissions on VPS host.
I read a lot of articles and forum posts, and there are two possible solutions: installing suPHP, and change of rights to WordPress folder.
Although suPHP should solve problem, it's said that it is slower, and that opcode cache can't be used on it.
With administrators of my VPS (its managed one), I tried second approach but without much success. The only thing that is solved is file uploading. What is left are automatic install/upgrade (asks for FTP), updates of files (like, .htaccess, wp-config.php etc), and W3TC cache clearing (cache is never deleted nor new one is made, which means
W3TC is unusable; note that old one was made on old shared hosting server).
My question is what do you do to solve this issue? Obviously people don't install suPHP since they can't use opcode cache, which means there are other solutions.