i guess for me it depends on the trip, time of year, and location. most stuff is like that i guess.
i currently live in Louisiana. flat water, no real portages, water's warm almost year round except for Dec-Feb. i mostly just wear water shoes, with a pair of cheap green pack boots for 'winter'.
my summer trips in the Adirondacks vary. in june-august, i bring the water shoes and a pair of low Merrill Ventilators, one for the canoe, the other for walking/portages. i don't believe in 'waterproof boots' or shoes, and you will drive yourself nuts trying to stay dry. thick, soft, high-quality wool socks are critical to comfort and warmth. my whole shoe thing dries quickly, and that's the key. doesn't matter if my feets get wet.
for fall trips to the Adirondacks, where the water's cold (sept/oct), i'll sub out the water shoes with the cheap green pack boots. again, the thick wool socks are important. in this case, you can portage in either the shoes or the rubber boots, and this becomes important if it's a really nasty muddy portage. i did the St Regis area last fall, and walked a very muddy "fish pond to long pond' portage (2 miles ish) in rubber boots. not the best walking footwear, but given the state of the trail (a running stream after 2 days of rain. sank up to mid calf and deeper in some spots), i did fine because of the thick socks.
hope that all made sense. rubber boots for cold weather, water shoes for hot.