It would be awesome to have a feature to Open From / Save to FTP/SFTP Server (such as offered by BBEDIT)
You put in the server credentials, and you are provided a list of files to work off of from the server. When you save a file it saves directly to the server so there is no need for an additional upload.
The current integration with Transmit (or other FTP client) is ok, but it has at least two major limitations:
1) every save gets uploaded - this is bad if one is developing on a local server and then uploading to a remote test or production server
2) using projects becomes kludgy (as discussed elsewhere)
There are several ways to work with remote files. Refere to the Projects section of the FAQ for how to do this.