No worries - I enjoy a good design discussion as well, and that was the spirit in which I posted...to some degree playing devil's advocate to offer food for thought.
I assumed as much about quest tracking - not perfect, but limited by platform, and if the list can be filtered by level range or area, and searched by name, it wouldn't necessarily be too bad to find the appropriate quests from a list.
You know though...it would be extremely cool if we could take screenshots of our quest log and map with quests tracked, have them loaded by the windows agent and then processed into the app. You know, simple binary image comparisons, adjusting for screen resolution, pulling out the quest rings and area shading from the maps, OCRing the quest names from the log screenshots. No problem, right?
Zone vs. seamless - I have to say at this point I'd probably draw the same conclusion you're leaning towards. The navigation with seamless probably isn't as bad as you think though, and it's a paradigm we're used to with other apps, like Google Maps. Pinch to zoom out, double tap on another area to zoom in and center...not too bad. I still don't see a clear winner either way, but because some instances will have to be in "zone" format, it seems to lend itself to using zones for everything - but maybe zones that are aware of their relative position in the world, so that if you're trying to display quest objectives for a location outside your current zone, it could possibly display arrows pointing out of the zone, like the radar map does, rather than just not showing the location indicator at all like the in-game parchment map does.
I understand the neighborhood problem, and agree with the basic idea of personal vs. shared/submitted points. The only issue with neighborhoods is that you'd need to be able to flag, at least with a note or something, which neighborhood that point is in. Even then, they might overlap/collide, which could be troublesome. Let's say you have two friends with houses at the same address in different neighborhoods....