He did make a very well-regarded, commercially unsuccessful 'cult hit' adaptation of a certain sci-fi franchise.
It is not well-regarded, even by Lynch himself and your statement is somewhat of an oxymoron. To this day, he still bristles whenever the subject of Dune comes up and prefers not to talk about it. Yes, it has a cult following, but by and large most people actively dislike that film.
I don't think a live action version should be attempted at all unless it is trying to bring something new and interesting and smart to the table and isn't just a rehash of everything in the series. It also needs to be in capable hands directorially. The only living directors that could feasibly pull this off are Denis Villeneuve, Steven Spielberg, Christopher Nolan, and Rian Johnson.
Pen Pen should either not be in the film at all or be in the film, but use a real penguin (not CGI) and play down its inherent ridiculousness. Anime tropes and general goofiness transferred to live action is a recipe for schlock and cringe.
There are other suggestions I could make, but it would be a waste of time and energy. Right now, the chances of a love action Evangelion movie being made ever stands at about 2%. If the GITS film is a hit, it goes up to about 7%.
I'd like to also remind you all that the most critically successful Hollywood film based off a manga or anime is a Tom Cruise movie.