I'm guessing you're considering for a 2 place trailer.... The fiberglass will be more aerodynamic if clamshell, like Wyelde mentioned. They are more contoured to the tops of the sleds, look good and tow well...
Depending on what you want to do with it..... If the weather is bad and you have to work on a sled, you won't have enough room to close the clamslell and work on a sled in there. Also, the walls in an aluminum trailer will have stronger corner posts, etc, where you can mount coat racks, helmet racks, oil/lube can racks, etc..
You may want to consider how far you're hauling your sled. Usually we have a 10-12 hour drive each way to get to where we sled.... What else do you want to haul with your sled? We haul tools, just in case, and throw all our gear in the trailer so we have more room in the truck, and our gear is always dry when we get to the hotel.
Personally, I own an all alum 4 place featherlite enclosed trailer. We use the trailer quite a bit since it's so easy to load/unload. Instead of leaving our sleds out where they can get stolen, tampered with or covered with ice, we pull them into the trailer each night, knowing out stuff is safe. Also, you can use an alum enclosure for more than just hauling sleds... ever have to move furniture? The taller height is very helpful.
Cheers, and good luck with which ever way you go.
My insane love of snowmobiling is the only thing that keeps me from going insane! Yes, if you see a 2011 snowmobile calendar at a sled show, that IS me on the cover.