IKEv2 VPN El Capitan 10.11
A little late , but I did get this working. 

In ipsec.conf, I had to update the ciphers and the rightauth. I'd prefer to use something better, but at the time it connects.

rightauth=eap-tls
ike=3des-sha1-modp1024
esp=3des-sha1-modp1024


BTW: even with connecting, I still get the above errors/warnings.

Update: I found that the mobileconfig profile needed for iOS can be used for OS X also, which will allow you to define and  update the encryption algorithm, integrity algorithm and diffiehellman group. You can read about all the config settings on Apple's Developer site. It looks like you can max everything out at at AES-256/SHA2-512/18 (modp_8192)