@GWG has put out a very customized version of his Twenty Sixteen Theme on Github. For those who have some development skills or are willing to look at examples to try changes themselves, the commit history of this particular theme is very enlightening and does a reasonable step-by-step job of providing snapshots of what he changed in Twenty Sixteen to make it more IndieWeb-friendly. For most themes, one may not want to go as far as he did to remove Post Formats in favor of Post Kinds for greater flexibility, but most of the rest is pretty useful and solid as an example if one is converting/forking other popular themes to make them more IndieWeb friendly.
There are a number of very IndieWeb-friendly themes and even child themes listed on the Themes page of the wiki. Most of these should “just work” though a few may have small bugs which could be filed to their respective repositories to improve them.
It’s generally recommended not to use the mf2 plugin with themes which are already very IndieWeb-friendly as it can cause issues or have unintended consequences. That plugin is generally better used when themes only have the minimal microformats v1 code which is added by WordPress core.
There are also lots of details and brainstorming for improving themes in general on the wiki page for WordPress/Development/#Themes.