I think BotW has come closest to my ideal tower system, though I honestly rather enjoyed the towers of AC and Far Cry... the problem with those latter ones was, first, that there's generally too many of them, and second, they're absolutely necessary.
Zelda's tower system is fun in that they primarily exist to get you way up there to spy out shrines and places to go that were intentionally placed within eye-shot, and also a wonderfully fun "fast travel" option from which you can usually paraglide wherever you'd like to go, during which you often find new places to visit. Otherwise, it mostly just shows the geography, leaving you to fill in the names of each little area.
Definitely the best system I've come across so far.