Which VPN protocol you choose will likely be based on a number of factors. Interoperability is one factor to consider. If you need a VPN solution that is interoperable with another firewall or router, especially one from another vendor, then IPsec may be the ideal protocol to use, since it is included with every VPN-capable device. Using IPsec will also prevent you from being locked into a particular product or vendor, is easier to configure than L2TP, and is about as easy to configure as OpenVPN. If interoperability is your main concern, you might consider OpenVPN, which is rapidly gaining traction, although it is not as ubiquitous as IPsec.
Another consideration is what type of authentication the protocol uses. IPsec ...