Wasn't so much money was the issue, though they did blow most of the budget early on, it was more that, Anno, the director and lead writer, kept changing his mind on what he wanted to do with the show and so they animators kept having to scrap things they were working on and start over, running right up against the horrendously tight schedule of TV.
Most episodes of the show would be recorded to a DigiBeta tape and sent to the broadcast studio a day ahead of time so the producers could review it and prepare the advertising schedule when it aired. Episode 24 there had to be delivered by bicycle courier and arrived literally 20 minutes before its air time. Leaving no time to be reviewed.
But that's why the last few, and especially the last couple, episodes suffered. Just not enough time to do anything spectacular on.
Which is why Anno cobbled together scenes and reanimated others and made the theatrical release of Death and Rebirth so that he could fund the End of Evangelion to give a proper ending to the series.
Not that it made much sense to audiences at the time.
That said, Mitsuo Iso's work on Asuka's fight scene was some of the best in the franchise with it being one of the few times the Evas got a decent sense of scale and weight.Okay, I'll go now.