I think she just straight up did not want to make another Matrix. She also did want to make a movie dealing with the grief she felt for her parents - and believe me, my criticisms of the movie are not leveled at her personally. If this was cathartic to her, by all means, I am happy she did what she did. The part of the movie that does connect to that element is actually really good. I think the movie could best be described as a beautiful 40 minutes' worth of compelling character drama, interspersed amid a poorly executed 2 hour blockbuster. It isn't a Zero. It's not Terminator Dark Fate or whatever. There's elements that do work, ideas that are interesting. But her heart wasn't in it beyond anything that directly involved Neo and Trinity.
The other main missing ingredients: Bill Pope (cinematography was inconsistent - sometimes nice, sometimes downright ugly) - Yuen Woo Ping (bad action scenes), Don Davis (new music monotonous, old music not used effectively - Neo and Trinity's love theme was absent!), Lily Wachowski. I know she wanted even less to do with this one, but maybe Lana should have waited until she was truly ready to come back. I don't know who had which ideas, but they worked together so much better than they do apart, clearly.
Also, bummer about Daniel "Guy from Future War" Bernhardt , who played Agent Johnson. He was in the movie as of test screenings and cast interviews last month,but was completely excised from the final cut. You can kind of see a gap in one action scene where he was meant to show up. Not exactly my favorite character or anything, but he seemed so happy to be back.