I'm assuming the core comes down to the different Scripts/Scenarios for instrumentality
- Yui's script— possibly benevolent
- SEELE's script — malevolent
- Gendo's script— malevolent, but results in Gendo reuniting his soul with Yui's
- Shinji's script — possibly benevolent, poorly thought out
- Misato/pirate script — NO INSTRUMENTALITY
In the TV series Gendo's script was followed to conclusion, the world's humans lost their bodies and individuality but Yui got to be immortal in Unit 01 in space. Gendo was unhappy because he didn't get to be with Yui. SEELE was happy even though they didn't get to be immortal because humanity became a hivemind so that was pretty close to their script.
In rebuild 2, Shinji goes Third Impact early and almost executes a feral script for instrumentality, but Kaworu halts him with a Spear so that it can be carried out later on SEELE's script. Time passes, SEELE has retracted into the monoliths so they can be immortal, Gendo is building EVA 13 so he can restart instrumental