Omit books 9, 11, 12, 14, 16, 25, 28, 36, 37, 39, 40, 42, 44.
If you want to leave out more, add 17, 24, 46, 47, MM1, MM2.
That leaves 44 books. KA said she thought Animorphs probably should have been ten books shorter, so that works.
That leaves us with these books (not listed in chronological order):
1, 2, 3, 4, 5 (Opening)
7, 8 (Kandrona arc)
AC, 13, HBC, 23, 34, 38 (Tobias's family story, Hork-Bajir story, Andalites emerge as potential antagonists)
15, 18 (Leeran war)
19, 29 (Yeerk Peace Movement)
20, 21, 22 (David trilogy)
10, 26, 27, MM3, MM4, EC, 48 (Ellimist/Crayak/Drode/Pemalites/Chee storylines)
32, 33, 43 (Anti-morphing ray, Taylor)
6, 31, 41 (Jake and Tom drama)
30, 35, Visser, 45 (Visser One storyline)
49, 50, 51, 52, 53, 54 (End of the war)
When looking at books to trim, I took more into account that what they strictly contributed to the overall story arc. If you look at it from that angle, a book like #3 isn't necessary. However, it would be pretty ridiculous to create the Animorphs story and leave out that material. The character of a boy trapped as a hawk was pretty darn unique, and people reading the series would likely be interested in how he's able to cope with the experience. It doesn't move the invasion story further much, but it's still one of the more valuable entries in the Animorphs series.
The facts and basic outline of the Animorphs story aren't what make it successful. It's how the story is told. Books like the Andalite and Hork-Bajir Chronicles were extremely engaging and moving. There's far more value to them than just what background info they contributed.