There are a few examples which REALLY make me scratch my head... for example, why didn't they build a single clone-trooper costume? They were all digital, but why?? Even in the scenes where they aren't wearing helmets, they've just tracked Temuera Morrison's head onto a digital clone-trooper body (horribly, by the way) or used an all digital head (even more horrible), which makes absolutely no sense, and is another huge waste of resources.
Or just take Padme falling out of the transporter onto the sand dune (in AOTC)... they've created digital sand and digital footprints in the sand... uhm... again... WHY?? Would it have been so expensive or logistically difficult to put a truckload of real sand onto the set? And again, in this scene Portman had to act with an all digital clone-trooper...
And if I remember correctly it wasn't Neeson alone complaining, it was McGregor as well... acting in front of nothing, towards nothing... I bet he's glad the trilogy is done.