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From 90 to 45! How?

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Because it sheds its husk to become lighter and faster and leaves the husk behind. It sacrifices toughness for flight and speed. Interestingly, both Ninjask and Shedinja have a base Defense of 45, exactly half of Nincada's.

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I agree. It defeats the point of Pokemon!
I really don't understand why I'm getting all this hostility here. I made an honest attempt to answer your question and explain it when you seemed confused by it and suddenly I'm an enemy of fun? What?
I think Dragonfrees theory sound perfectly viable. I we just assume it's new husk is less effective (weigh more/provide less armour) the lost Defense and increased weight makes sense. If anything, applying logic, math and theories from other field of studies makes more fun and engaging. Finding proof that these games are smarter than simple kids games whose only explanation is "Game Freak wanted it that way" is far from killing the point of Pokemon.
Well, look at it from foofles's point of view it's right. Ba then!
Completely agree that applying physics etc. to Pokémon is good fun and a lot more interesting than just automatically waving everything away with "You can't bring logic into a Pokémon game." Obviously it 's a game, and it's not going to make perfect sense in every way and it doesn't have to - but that doesn't mean it isn't fun to try to make sense of it anyway!

I still stand by my point that the new husk /isn't/ just less effective, though. As I explained above, Ninjask actually weighs a lot less /given its size/ than Nincada does - it's less dense overall. If Ninjask's armor were as heavy as Nincada's (and the rest of its body also had roughly the same composition), it would weigh almost twice as much as it actually does according to the Pokédex, because Ninjask is also quite a bit bigger than Nincada. So Ninjask's armor really does appear to be much lighter in exchange for its poorer defensive capabilities - which makes a lot more sense, because developing armor that's both heavier and worse at protection upon evolution would be pretty counterproductive.
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I personally believe that Nincada's Defense is just naturally high, but when it evolves, it splits into two parts: Ninjask and Shedinja. Its high Defense as a young Pokemon must be split equally between its two evolutions to keep a balance. Also, Nincada's priority was storing power for evolution, so it had to be defensive often, while Ninjask's only priority is to go fast. Shedinja has no soul and no priorities. Period. It just maintains the balance between the two. (I mean, seriously. Imagine a Ninjask that could actually take hits well... With that high Speed and Swords Dance, it'd be GG to the metagame.)

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