Very important during training for Colorado Trail trips, that you dial-in your shoes (and socks). Avoid blisters if you can; they make hiking much harder to enjoy. Find the right fit, roominess, and breathability (etc) that works best for your feet. Well in advance of your trip, try different shoes until you have some winners. Then resist the common temptation to change your footwear right before your trip starts.
Trail Runners (or similar) are the choice of most CT hikers. Experienced hikers swear by them because, finding the right trail runners can limit blisters. Lightweight, they are sufficient for the relatively friendly tread. (The CT has little talus-like surface.) Though they offer little ankle support, experienced hikers post that training strengthens ankles sufficiently, and sometimes discuss trekking poles as adding enough stability to eliminate the need for any shoe-provided ankle support. Trail runners dry more quickly than boots, some faster than others. Low-top, they capture less of your heat and can reduce sweating to keep your feet drier. Cooler and drier feet usually means fewer blisters.
Boots are chosen when the hiker feels the need for better ankle support. The mid- or high-top ones, when laced tight enough, can hug your ankle and add a little support. The soles are generally stiffer and can help the hiker who’s not able to train past the sole bruising some struggle with. Though experienced hikers consider boots overkill for the CT, good choice in footwear is whatever works best for you.
Waterproof or not is a matter of personal choice. “Which is best?” is often debated energetically. Waterproof are appreciated in the rain. But users report that waterproof footwear takes longer to dry, and that it’s hotter. Best to try different styles until you find what’s working best for you.