Dragon's Dogma had I think up to 3 custom waypoints you could place. Basically the game didn't have some big arrow pointing you towards your location, nor did it tell you the precise route how to get there, the waypoint marker would just sit on the edge of the mini-map based on which direction it was from your current position.
I thought it was perfect (Then again Dragon's Dogma did ALOT of things right, like holy shit). If I ran into a cool location or creature I couldn't quite beat, I'd just pop a waypoint down and come back to it. I think the notes part is probably unnecessary and I honestly can't think of a single game that I've seen do that - apart from leaving messages in the Souls' games, but that's not the same thing.
Frankly I'm not going to fret, custom waypoints is a pretty basic feature that just about every open world game has these days, no doubt TW3 will have it. It doesn't really need much customization, just as long as you can plop at least one down on the map, it's all good.
I think for TW3 though I'll probably have a little notepad next to me to jot down locations to come back to and other bits and pieces, then I don't even have to tab out of the game.