It is very worth it to have a good sub. The one that came with that Klipsch set is not very good. That's why is sounds "boomy" to your wife. Have you calibrated your system? ran Audyssey?
Go 2.1, for now. but don't skimp on the sub... it's going to do the hardest work, and thereby take strain off your receiver, and allow your speakers to handle the higher notes, like from 80hz and up. For mainly movies, I would look for something that handles at least down to the low to mid 20 hz range. Don't buy cheap tools.
mods, can we have a 'dislike' button ?