IPsec VPN on iOS with Fortitoken authorize

Speaking in general (not just about iOS):

If you're using IKEv1 with XAUTH, then any client should work, as long as its developer bothered to implement a way to prompt the user for input when mode-config XAUTH prompt (asking for a token in this case) arrives.

If we're talking IKEv2 with EAP, 2FA with FTK will be exclusively compatible with FortiClient, and no other client. There is (or was) no standard for it, so it is implemented in a custom way (3rd party clients not expected to understand it).

There is also one alternative approach you can try, which is appending the OTP code to the password, i.e. logging in like this:

username: jdoe
password: mypassword123456 ("123456" being the OTP code generated by FortiToken)

FortiGate and FortiAuthenticator support this for situations where the client may not be capable of providing a separate prompt for 2FA. Note that if you're using MSCHAPv2 or similar auth method, this will not work.