If I am using the small front chain ring, I shouldn't use the 2 smallest rear cogs. If I am using the middle chain ring, I shouldn't use the largest and smallest cog. If I am using the largest chain ring, I shouldn't use the 2 largest rear cogs. I just lost 6 speeds!!
Actually, no, you didn't lose 6 speeds. Those crosschained "speeds" merely duplicate the same speeds available in other non-crosschained gear combos. And they do it in a bad way, with chain kink (extra stress on the gear teeth), chain rub, and extra stress on the rear derailleur.
As far as building lockouts into the shifters to prevent crosschaining, it would just add complexity and weight to a shifter system, though I'm sure entry-level riders would appreciate such a feature.