This happens, exactly as described, to me too. VPN over 3/4G/LTE is fine.
VPN over WiFi gets around 0.3Mbps
WiFi alone is 6Mbps
VPN over 4G is 8Mbps
In addition, if I connect to a WiFi that has a built in VPN client (i.e. with the VPN client handled in the router) the iPhone 5 goes down to 0.3Mbps again. Other connections (Win 7, Mac OSX 10.8, iPhone 4) all get 5Mbps.
Didn't earlier versions of iPhone have separate processor, etc. for comms and the new iPhone just has the single chip? I wonder if the VPN overhead isn't being handled as efficiently now as before? Maybe just a simple prority fix?
Same results for PPTP, L2TP, IPSec, OpenVPN. Looks like something wrong in the iPhone 5 (or iOS 6 and 6.1). If so, come on Apple own up so we can stop running in circles and just sit and wait for the fix (or the iPhone 6).
If anyone has iPhone 5 and gets good speeds over WiFi and VPN, please post (and include the type of VPN you use etc.) Then I can maybe go in a swap mine (again) so that I get one that works.