Like Martin, I'm going to assume you meant to exclude Ghibli as a whole since you didn't include any Takahata and I think I remember you being a fan of some of them. That, and you have Miyazaki's pre-Ghibli Lupin on there.
1. Ruben Brandt, a gyujto / Ruben Brandt, Collector (Milorad Krstic, 2018)
2. Les triplettes de Belleville / The Triplets of Belleville (Sylvain Chomet, 2003)
3. Ookami kodomo no Ame to Yuki / Wolf Children (Mamoru Hosoda, 2012)
4. Mirai no Mirai / Mirai (Mamoru Hosoda, 2018)
5. L'homme qui plantait des arbres / The Man Who Planted Trees (Frédéric Back, 1987)
6. Kôkaku Kidôtai / Ghost in the Shell (Mamoru Oshii, 1995)
7. Pâfekuto burû / Perfect Blue (Satoshi Kon, 1997)
8. Louise en hiver / Louise by the Shore (Jean-François Laguionie, 2016)
9. Tehran Tabu (Ali Soozandeh, 2017)
10. Tout en haut du monde / Long Way North (Rémi Chayé, 2015)
11. Kubo and the Two Strings (Travis Knight, 2016)
12. Tower (Keith Maitland, 2016)
13. World of Tomorrow (Don Hertzfeldt, 2015)
14. Spider-Man: Into the Spider-Verse (Peter Ramsey, Rodney Rothman & Bob Persichetti, 2018)
15. Anomalisa (Charlie Kaufman & Duke Johnson, 2015)
16. Interstella 5555: The 5tory of the 5ecret 5tar 5ystem (Kazuhisa Takenôchi & Leiji Matsumoto, 2003)
17. It's Such a Beautiful Day (Don Hertfeldt, 2012)
18. Akira (Katsuhiro Ôtomo, 1988)
19. Shin seiki Evangelion Gekijô-ban: Air/Magokoro wo, kimi ni / The End of Evangelion (Hideaki Anno & Kazuya Tsurumaki, 1997)
20. Ma vie de Courgette / My Life as a Zucchini (Claude Barras, 2016)
Honorable mentions: Watership Down, Adama, Wolfwalkers