Why did Alphonse lose everything?
Alphonse was shown more of the truth than Edward, however he forgot it at the beginning of Brotherhood. Only towards the end did he remember. Thus, seeing more of it warrants a greater toll.

Also, the truth takes from you that which is most ironic (which is why it is such a cruel thing); for example, Mustang had his sight taken as he had his 'sights' set on being Fuhrer. Alphonse had his entire body taken as he wanted to feel his Mother's hugs and warmth. Having his body taken means that can't happen anymore.