It's something I wanted to post with my older suggestions, but I forgot. Anyway, here is a low-priority suggestion: Object Collision Mask.
Haven't you ever had objects with a small sprite but wanted the collision detection to be larger? Or haven't you ever had objects you don't want to have precise collision checking while the rest of the game has? This could be fixed with an object collision mask, where you draw the collision area the same way you draw hotspots, only you would do it in the object editor instead. Maybe a "object uses collision mask" option for each object would be also good.
This can be already done by playing a little, but this feature would be a faster and cleaner way,
Hmm, how about a way of disabling the pixel-perfect click detection on a per-object basis? That way, you could just turn off pixel-perfect and import a sprite with transparent edges large enough for your target hit test area.