I know exactly what you mean. it seems like it takes forever to 'update remote manifest' etc. That's why I only use WP publish to web when I have to. I can upload hundreds of files with FileZilla (or probably any other good FTP client) in the time it takes WP to upload 10.

For most uploads I use FileZilla. Unless an image (picture) is regenerated by WP I can upload any page that I published to disk with FileZilla. It literally uploads in about a second. I have uploaded hundreds of pages at a time in a fraction of the time that WP publish to web takes.

I also have WP generate an 'updated' date at the bottom of a page so I can easily see that the latest page was updated online when I check to make sure the uploaded file still looks right (sometimes the preview looks fine but what I see online doesn't look the same).

I mention images because they are the only situations that I use WP publish to disk (and occasionally for an untended overnight publish all pages (with delete to get rid of any old unused files). I'm not sure what the problem with images is but I had a problem with this in the past.