One of my main problems is having to keep clicking repeatedly in order to get the right amount of tiles, or objects (when I use water). So maybe you could drag a box or circle?

and like yeah, the overlapping it even has gaps aligned with the grid sometimes, just annoying...

you should make a background with the tile sets, thats what i did in the rpg im working on right now. I went into paint and i copied and pasted the grass tile onto my new picture then i saved it as a background on my game maker file, then on the room i added the background and didn't make it stretched becuz i looked really weird. Also if you were adding water or anything, i don't think there is any other way. I wish it could be like objects where you hold down shift and it creates multiple objects. In Game Maker 8 they should add that as one of the extra things for both the free and pro editions of game maker.

and so the grid isn't used as a separator by even a mega pixel which I can very easily notice and pick up quite quickly unless I have personally put them into separate positions on the screen myself...

Actually, i've had that same problem several times myself. One very simple way around it is to make a 'room parent' as such to duplicate, so that you don't have to constantly put borders around the rooms. But i have always liked the idea of dragging a box around certain areas to save time. I'm so glad someone brought it up.