Well, two schools of thought on this:
1. The LE's and the show as a whole were slow sellers, and they'd like to not clearance out all those singles just yet if they don't have to (see: Haruhi Suzumiya, where we are just now seeing the remainders of the singles get flushed out at bargain prices.)
2. Singles are dead and LEs like Lucky Star's are what killed it. At least do some Funimation style half-season boxes, or even just half-season bundles. No one is going to buy it otherwise now. Really, they should just cut to the denouement and do a $60-70 msrp box now, come back with a $30-40 msrp single-case thick boxset in another 18 months, maybe at the same time as a blu-ray boxset.
As it stanRAB, Bandai still does too many SKUs for one show. Stop doing LEs - there isn't enough audience to split the sales like that any more.