I don't understand the problem with wells.
Then again, I only ever use them for sanitation, as dwarves really should never be drinking water anyway.
The way I deal with wells, is to have a 2 level cistern that has only the bottom level filled with water, and only to 4/7 deep. That's enough for a bucket to work correctly, but too shallow for a dwarf to drown if they drunkenly fall in.
Inside the cistern are steps leading back up into the fortress. The cistern is automatically filled at 4/7 using a pressure plate linked to a floodgate, which is in the floor above the 4/7 water, so it pours down, allowing more efficient use of pressurized water to fill the cistern. Before passing the floodgate, it gets sprayed through a "filter" made of fortifications, ensuring aquatic terrors of the deep never make it to the cistern.
I don't have any major problems to report with such setups, but I tend to only make them for the hospital zones where clean, fresh water is a requirement for proper function. (Though dwarves often abuse their hospital privileges to take baths in the hospital.)
Really, you don't want dwarves near the wells anyway. "Filth" from bathing builds up around them in my experience. (Why I try to keep dwarves out of the hospital if I can-- sick dwarves wit open wounds aren't something that should make contact with said filth.) Dwarves walking through the filth will get filth on them, then be driven to bathe, leading to an endless queue of dwarves at the well to get clean, and subsequently dirty again.
Using a simple showering system, or dunk tank, works better for cleaning, as the filth is easier to deal with that way.
I haven't had a dwarf drown in a well in a very long time...