If you're using a layer type target either one will be difficult to remove. But IMO there is no comparison between the two. Carbon is the better of the two hands down. It is tougher than aluminum and they are either good or busted. Aluminum arrows are a pain. They have to constantly be checked for straightness and straightened out. Otherwise they fly all over the place. Not sure but I believe carbon arrow stop oscillating quicker then aluminum ones and their thinner diameter gives you greater penetration.
Get carbons and a bag target that can stop them out of your crossbow.