When I first attempted to create a remote VPN configuration on a Cisco ASA with a L2TP/IPSEC config I ran into similar problems as described in the post. However after several weeks of work I eventually was able to configure a L2TP/IPSEC config that successfully supported MSCHAP V2 password encryption that authenticated against Active Directory. Basically native MS Windows VPN client on all platforms. The key pieces were that I used RADIUS on the ASA tunnel configuration and configured Microsoft Network Policy Server as a RADIUS server with group policies. The important configuration parameters that need to be enabled on the Cisco ASA follow. Hope this helps.
tunnel-group DefaultRAGroup general-attributes
tunnel-group DefaultRAGroup ppp-attributes