If I were you, I'd settle with the compact flash. 16 gigabytes is a lot of storage on a tiny Amiga.
My A600 has a 40 gig drive, but I'm currently only using 3 gigs of it, and the partitioned space is about 14% full IIRC. I have everything I need installed, too.
Oh, and accessing anything beyond 4 gigs can be quite a struggle. Unless you want to install thousands of games, go with the CF.
