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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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But Ninjask is heavier. You're saying its organs grow bigger or something?
Ninjask is bigger in general. A Ninjask-sized Nincada that didn't shed its skin would probably be heavier. (Though you should always take Pokémon weights as shown in the Pokédex with a grain of salt - given the provided size and weight of Wailord, for instance, it's actually lighter than air and should float upwards like a balloon.)
Nincada =5.5kg
Ninjask = 12kg
Dragonfree, how does one even determine the density of Wailord? :l
Yes, but also Nincada = 0.5m and Ninjask = 0.8m. Ninjask is bigger by a factor of 1.6. A 0.8m Nincada, assuming Nincada and Ninjask's shapes are roughly the same, would be 1.6^3 times heavier than a 0.5m one, or just over four times - in other words, a Ninjask-sized Nincada would be over 22kg. Ninjask is only just over half of that - much lighter than if the Nincada just grew without shedding its skin.
What SM said. It weighs what, 450 kgs and floats?
Wailord is roughly cylindrical, so given the length and weight given in the Pokédex, you can calculate an approximation of its volume. I didn't do the math myself, admittedly; I saw it here: http://tcodquotes.tumblr.com/post/31515457970

Although I misremembered the conclusion slightly; it is somewhat denser than air, but because part of it is clearly flesh/water and those are much more dense, it must contain a lighter-than air gas to balance them out in order to end up at its provided weight.
k dude you cant bring logic into a pokemon game :l.
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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Also, shedinja is a piece of dry skin. Thus it's low defences.
And ninjask has no more protection left.
Shedinja doesn't have dry skin as ability cuz no one would use it.