Windows has supported IPsec/L2TP VPNs for more than a decade, and PPTP hasn't been the default in years. Windows also supports SSL VPNs. All current Windows VPN protocols are fully standards-compliant. The problem likely has NOTHING to do with Windows and everything to do with the extra things that the Cisco VPN client is doing beyond just standard IKE negotiation, etc. In order to even possibly use the native client rather than the Cisco client, you'll need to know the authentication and encryption algorithms and mechanisms in use, the keying parameters, any RADIUS attributes that may be used, etc.
+1 This is correct. Cisco used to use IPSec, but has switched to SSL (with the AnyConnect client). – Ian Boyd – 2011-07-26T15:23:52.170
3Windows allows L2TP/IPsec, SSTP, PPTP and IKEv2. It is not restricted to PPTP. (At least, Windows 7.) – ZachB – 2012-07-25T12:33:38.607
Windows has supported L2tp over IPsec since at least Windows XP. – ThomasMcLeod – 2013-07-14T05:20:46.723