Yes, but WWE can't seem to book Taker into a fued with Shawn or HHH without involving the other in some capacity, almost involuntarily. There's plenty to work with for a storyline between those two and its clear that its what WWE would rather do (Taker gets priority pretty much out of obligation).
The fact that it was done before eight years ago probably doesn't hold much weight. For Taker/HHH they've totally ignored their WM match from 2001, I don't see why they couldn't brush over HBK/HHH from 2002 as well. WWE have been appealing to the newer generation of fans with these fueds, so this Shawn/HHH idea isn't that crazy.