Attack form has loads of attack and sp.attack.
Speed is the fastest Pokemon of all time.
What Deoxys lacks in defense compared to Shuckle, it makes up for in higher HP and offensive stats, nice speed compared to most walls, and a great movepool.
HP is very important in defense (Just look at Shedinja.)
That's how GameFreak wanted it. We don't know why.
Because "a lot" is not the same as "more than everyone else". There is nothing that says Deoxys has to have the highest defense.
But Deoxys is clearly better because its other stats are much better than Shuckle. Its HP means it can easily take more hits than Shuckle.