I agree...
I think this is a very good 3D game, Except for one fact. The box fact.
My suggestion of fixing this and still haveing the clues would be...
When ever you click on something have the box at the bottom, and stay there for about 5 or 8 seconds( depending on the text ), then fade out.
Overall I think you need some sound to. There are plenty of good artist out there in the AP ( audio portal ). Also, the 3D effect was good. I found it sorta anoying and difficult to look at though, due to the brightness and fuzzeyness. If that Could be fixed somehow. Then this would be a awesomer game then it was in the first place. Nice job man.