I completely agree with Matt about the “warm up”. There is definitely a “break in” period from Waterton Canyon to Kenosha Pass, where one can acclimate over 4-6 sections of the trail. Bugs are really dependent on the water/snowmelt of certain sections, and are variable. Either direction, be prepared not to see too many other people. (With the exception of mountain bikers in the early sections) This is one lightly used trail. That being said, you will definitely find that fewer people hike the CT South to North than the other direction. About the only negative I can say about a N > S start in late June is the early heat. I have hiked with many thru hikers on the opening sections during June/July, and it can be an oven. Other than that, by going South, you will probably have better water resources as the summer progresses. We had plenty of snow this winter (I live < 2 miles from Waterton Canyon), so water shouldn’t be too much of a problem. As for fall foliage, a later start in either direction could help, although you risk the chance of snow if you start too late. I have done several fall hikes on the CT, and it is a special season, but I was only travelling 100 miles or so. One approach that may fit all of your requirements may be to do a “flip-flop”. I’ve been toying with the idea of doing that.
TrailGuy