Honestly the changes are all welcome and good additions. Waypoints in particular just feel really good to use and the diagonal bridges was also something that I didn't know I really wanted.
I struggle with the "pave everything" connundrum. On one hand, you probably want to avoid the game beeing this easily cheesed. On the other hand, it's a single player game, so who cares? I don't want the experience of legitimate player to get worse because people like me find ways of cheesing the game. So yeah, up to you if you want to play around with the number of rows the player gets to make it harder for people like me.