I agree with the OP that this new targeting method is bad; I'd say awful. It makes it even more probable that admins will deploy to entire domains instead of specific machines. Also, it doesn't seem to be implemented consistently. Check Configurations/Message Box for example. You CAN exclude specific Computers but can't TARGET specific Computers.
I understand ME's interest in pleasing all or most of its customers, but accommodating every feature request without considering negative usability impact can lead to changes like this to the detriment of the product for everyone else.
My 2 cents.