Yes, all boils down to THIS as my main gripe with the hero. Its so easy to lose him in a teamfight or waste mana/health fighting the wrong one. But I cant think of anything to fix this without hurting the other illusion users (Naga, CK, manta pickers...)
Like I said, I think it would be a very reasonable change to have something like Bounty Hunter's track arrow appear over the real PL if you have detection on an area. It's pretty absurd that late game PL becomes virtually immune to strong single-target abilities like Doom, BR Lasso, etc. because you can't really be sure that you're using it on a proper target. You can't really afford to simply roll the dice with those abilities and hope you're targeting the right one.