I used to have frequent problems with Evo, usually when transferring the tinymce plugin files. I had a problem once with Revo, then stopped using FTP to transfer all the files.
Now I use the install.php script, which works fine, except for advanced installations where things have been moved or renamed.
But updating an advanced installation is complicated in any case, since the core directory has to be moved and any other folders that were renamed have to be manually updated anyway.
http://www.sepiariver.ca/blog/modx-web/upgrading-modx-advanced-installs
But at least they are all unzipped and in place in their default locations, so it isn't difficult to get the installation ready to run update.
I'm working on an advanced installation/update version that will ask you where you want the core directory on a new installation, moving it there before forwarding you to Setup. On an update, it will scan the config.core.php file to find where the new core files should go and what the name of the config.inc.php file should be. It will then scan the config.inc.php file to find out what the names of the assets, controllers and manager folders are, and move the new files into place if they are customized.