Waypoint management could be improved. Seems most features of TF center around tracks, which are cool, but I still use waypoints quite a bit.
First, when downloading waypoints from a GPS, it would be nice if TF let you choose the points you want to import and select a file to put them in - much like the dialog you get when downloading tracks. I store a lot of waypoints in my GPS, but usually I only want to download the ones from my most recent trip into TF. So as TF is now I have to download all of the waypoints and then delete the ones I don't want.
I would also like to be able to cut/copy and paste waypoints between GPX files. Sometimes I put a waypoint in the wrong file and it would be slick to be able to select that waypoint, cut it then paste it into another file, rather than have to edit the GPX files manually.
It would also be nice to have a way to project a waypoint to the elevation (DEM) data to use that elevation for the waypoint. GPS doesn't measure elevation very accurately, so the DEM data should be better. Not a terribly useful feature, but might have some uses.