Only thing that Shaft really need to fix is crazy schedule and staff-pressure. Last months, they suddenly started
recruiting animators and producers, I guess this was the reason. Producer one now seems to be filled, but they are still recruiting more animators.
They already have facility to do 2 project at once. The problem is the number of staffs/key animators, which was NEVER fixed since Team Shinbo's joining.
However, one of the major reason is their animation style. Unlike anyone think, Shaft's direction takes quite a lot of effort in order to animate, due to their unusual obsession towards BG art in particular; one BG arts are only to be used for less than a second and they are giving full effort to every single of them. Camera-panning scenes are generally much trickier and harder than normal animation (except sakuga sequences).
Edited; On the side note, when they are animating Bakemonogatari and Zan Sayonara Zetsubou Sensei, they were drawing key-animations like 'A DAY BEFORE' episode's airing. Nevertheless, they
successfullyactually managed to finish both series on time
except the web-cast, with Bakemonogatari's huge success. At least, Shaft does much more consistent animations (even with this impossible schedule) than another certain A studio which ruined adaptation of BL game legend and SD studio which does horrible animation all the time.