As Wikipedia reports, GAINAX was, at the time, not a wealthy production studio. Evangelion was begun after a film project was dropped due to lack of money and the studio was dropping various parts of their business to stay afloat. The complicated mech designs of the Eva series were originally deemed to be too complicated for merchandising, the accompanying manga was initially viewed poorly, and funding sources pulled out one after another while the series aired. As the show became too expensive to animate from episode to episode, more and more earlier footage was re-used. This should have been a disastrous choice, but the way the re-used footage was incorporated into the internal struggle episodes is a large part of what has made Evangelion so memorable.
For what it's worth this blog assumed back in the day that the long pregnant pauses between tortured, painfully communicating characters were completely intentional.