I will likely use Libreswan for both L2TP/IPsec and IKEv2, and give the user a choice between those options at installation. L2TP/IPsec support is still a little more ubiquitous, but IKEv2 will be set up by default. It's a much better protocol with significantly less legacy baggage.
Your comments on Tor are thought-provoking too. I can look into making that optional as well, either through a prompt or command-line flag.
Thanks for the feedback! Let me know if you have any other suggestions.