VNC over SSH should be as secure as you need, but it's never likely to be as performant as RDP.
In the 90's when everything was made of lines and rectangles, you're right that this deep integration made RDP perform much much better.
Now though, nearly all applications are composited bitmaps (webviews, opengl surfaces, etc). There isn't much scope for sending the raw draw calls over the wire anymore, and instead using some video codec to send the surfaces as bitmaps, and then compositing on the client is about the best you can do.
VNC doesn't even do that though...
In all seriousness though it's useful if you use VNC just to remote monitor a screen and want to leave it open indefinitely.
Also RDP uses TCP and UDP which makes it bad for SSH tunnelling, as opposed to VNC which is TCP only and easy to tunnel.
With TCP multi-megabyte buffers can end up forming and when you've shoved data into TCP there's no way to cancel sending it.
- Compile it yourself. The package that comes with your distribution is bad and has things like copy/paste disabled.
- Configuration of authentication takes some effort.