I only hate the ones who's plots have been used before , like #39. That's the only one I don't really like. the others, except #24 and, to a lesser extent, #42 (although the reasons are a bit more personal. I hate the helmacrons), I like.
so the only books I would take out are #39, and #24. #42...well I don't like the helmacrons but the idea of going inside marco was pretty good.
though if I had to shorten to about 30 books...
#1 (the first book, duh)
#4 (they meet ax)
#5 (they meet visser one)
#7 (they meet the ellimist)
#8 (seerow's kindness)
#10 (the chee)
#13 (tobias gets his morphing powers back)
#19 (the ypm)
#20 (they get the blue box)
#21 (and of course if you have 20, you need 21 and 22)
#22
#23 (elfangor is tobias's father)
#26 (they meet crayak)
#45 (beginning of the final arc, and marco's dad finds out, and get marco's mom back)
#49 (the yeerks find out they're humans)
#50 (the auxiliaries)
#51 (the governor)
#52 (destroy the yeerk pool)
#53 (second to last book)
#54 (last book)
no megamorphs, no chronicles
yeah...really boring...