There is actually a third approach. The asp.net membership functionality is based on the provider model. You can write a custom provider, thus being able to provide your own implementation for how the data is stored, but retaining much of the benefit of asp.net membership.
Some articles on the subject:
http://msdn.microsoft.com/en-us/library/f1kyba5e.aspx
http://www.asp.net/learn/videos/video-189.aspx
http://www.15seconds.com/issue/050216.htm
http://davidhayden.com/blog/dave/archive/2007/10/11/CreateCustomMembershipProviderASPNETWebsiteSecurity.aspx
