I'm not a map maker but i've been reading these forums quite awhile now and I'm fairly sure most of your problem can be resolved by redoing those parts of your map. Make sure you paint at least 2 pixels wide where stuff should transition, where the grass juts out into the water and looks like crap or where the water comes into the grass bank and looks like crap is possibly only 1 tile wide and can't transition.
I don't see anything wrong with the right-side 2nd down picture where you have 3 things circled... then again that's probably my extreme lack of artistic talent showing through
