A way of controlling globally the spawn rate of specials would be nice. I may look into that at some point.
You can define alternate mapgens for each tile, so it might be advantageous to try and keep buildings inside one omap square as possible so that the arrangement can be semi-random.
I don’t like how the shops share a double wide wall, single looks better, but a little gap in between two would make a nice alley. East of church could be a cemetary, a daycare would fit, or you could move the park over there, add a gazebo and some playground stuff. I’d try to arrange the grocery store to open southwards, towards the other shops, and try to get the parking lot down that way as well, maybe making the grocery store smaller in the process. A dollar general type store would be a nice addition or maybe an alternate. Small towns usually have at least one dive bar, down in the southwest corner next to the fast food restaurant might be a good place for it. The other restaurant could have the counter shortened a little bit to make room for more tables in the corner. You could split the motel office area up into main office, back office, laundry room to use up the extra space, also some motel rooms could be two single beds, and maybe use tables instead of counters and throw in dressers. Might be able to fit a small school in along the sides? Salon should have a counter with cash register, and display racks for beauty supplies. I’d add a fence and some busted cars around the outside of the garage.
If the area is going to be irradiated, I would try to make sure there is some indication that the place is radioactive. Maybe have dead bodies around with geiger counters and unwrapped radiation badges. Radioactive gas could seep out of the sewers periodicaly (not sure how to pull that off without digging into the code), or maybe include a new specifically radiogenic monster, but the player would need some way to know they were associated with radiation; something like the ghouls from fallout.
Side note, you might be able to pull the motel out and make it into its own special so that it pops up normally, that way it won’t be a dead giveaway when you see one.