I also really hate the default behaviour of having certain things checked, then having to uncheck the stuff I don't need to find a more limited subset, then select the thing I want. This is mostly a problem when doing a lot of trigger work.
I think a better approach would be to use drop down menus that group things together. You could then have logical groupings of item types, and the preview window could be a lot bigger too. Here's an example of what I mean:


I realise that this could be a lot of work and that it doesn't account for the Add/replace screens. Those kind of work better because the checkbox choices are more logical. I think the drop down works better for the object selection screen because it's highly unlikely that you ever need to see triggers and items or monsters and triggers at the same time.
(Note that the categories I put in the drop down would obviouly reflect whatever you were doing at the time, and unapplicable categories would be removed, as you do at the moment).
One of the reasons for doing this is to also remove all the trigger stuff from the current FLOOR category. I think it's really illogical to group them in that way -- why should a floor trigger be in the same group as a pit or stairway, just because it's on the floor? I really think all triggers and mechanics stuff should go together.