We ride a 1999 RT road frame, and I think that everything on it has been worn out and replaced at least once (it began life as a 1992 model and Cannondale replaced the frame in '99 because the dropouts were misaligned). I take that back- the original Suntour front derailleur is still going strong and shows no sign of giving up the ghost

I feel like the only thing that truly needs to be upgraded on the Cannondale road models is the wheels. Once you've done that, you will have a good riding machine that can be upgraded at your leisure, or as things need replacing.

I would recommend staying with bar-end shifters if that's what your bike has- they are much less hassle than STI, and they can be used to good advantage in friction mode. Just my opinion though.

Rick