My pet peeve would be how Region IDs can't use the same Terrain tools as the maps --- no rectangle, circle or flood fill. It makes creating world maps a LOT more tedious than it should be.
For mapping, I think XPs map logic made more sense --- multiple tile layers and no autotiles. Autotiles are a good idea but make creating tiles far more difficult as Sharm already mentioned. They also need special handling to look good in more interesting cases (shift click mapping).
I think an ideal mapping system would use the Region IDs, Terrain IDs and Move Routes as separate, specialized layers, and have at least 3, up to 5 maybe map layers of normal tiles. And in all cases, the powerful map drawing tools would work the same --- flood fill, rectangle, circle, etc. For Events, you could then say "Event 5 use Move Route 10"
But I'm getting more into the "Features Desired in the Next RPG Maker" thread so I'll stop there.