The old Cannondale touring bikes (and the current ones) are excellent bikes. Depending on what changes you want, it might be relatively inexpensive.
Regarding the threaded headset.... there might be a question about your terminology. The headset is the bearing used to permit the fork to rotate, and is chosen based on whether the fork is threaded (the traditional style, which uses a quill stem), or threadless (which uses the "Aheadset" style of stem).
Either one works fine, but there's no real functional advantage of one over the other. Each has its own advantages and disadvantages. What sort of improvement were you hoping for?
Regarding the "suicide shifters"... Is this a reference to downtube shifters, or to stem-mounted shifters?
... oh.. are we talking about drop bars, or straight bars, ala' MTB's?
If it's drop bars, which the bike came with, then there are a number of options:
1. bar-end shifters. These fit into the ends of the handlebars, and are considered easier to reach than downtube shifters. These are generally favored for touring bikes, since they tend to do a better job of shifting on triple cranks. The shifters cost around $50 or so(?), and usually come with cable stops that attach to the fittings that your downtube shifters mount on. These are sold in either 8 speed or 9 speed versions.
2. Integrated shift/brake levers (STI for Shimano, or Ergo for Campagnolo). These are standard for most road bikes nowdays, due to ..... well, I'm not sure why. I think people prefer to not take their hands off the handlebars. These are more expensive than bar-end shifters, weigh more, and are more fragile/delicate/failure-prone. If your Cannondale has cantilever brakes, then it's harder to make the integrated levers work with them (these new style levers don't pull as much cable as the old brake levers). If your Cannondale has V-brakes, then you'll need a gadget like the Travel-Agent to allow the levers to pull enough cable.
The STI levers don't shift the front derailleur as well on a triple crank, but Shimano does make cranks that are moderately well suited for touring. Campagnolo levers do shift well on a triple, but Campagnolo doesn't make a triple crank that's suitable for touring. Oh.. you have to use Shimano shifters with Shimano cranks, and Campagnolo levers with Campagnolo cranks (according to them).
In general, if you feel the urge to change things around, you might as well. It's always fun to try something new. However, be aware that Shimano and Campy really aren't addressing the touring market, and that the older equipment might actually perform better. A good guide is to see how manufacturers are spec'ing their touring bikes now. Especially check Bruce Gordon's offering... he does the best job of setting up a touring bike.
And in the interest of full disclosure, my three-year-old touring bike is equipped with a 20 year old crankset, 25 year old derailleurs, 15 year old pedals, and new Shimano XT hubs.
These are all the parts that I feel perform best for touring and bike commuting. And I use downtube shifters (very reliable, and no extra cables going up to the handlebars that make it difficult to pack in a S&S case).
The bike has about 15,000 miles on it so far, and is doing fine.
Steve K.