There is so much accumulated cruft to SSL/TLS and the implemented x509 certificate scheme that to me, as a noob who knows nothing about crypto i.e. the average user, the easier path is to scrap all that ("shed all legacy" junk) and focus on learning a few things that are both flexible and known to be useful. I believe NaCl fits this role.
I have some basic UNIX-like utilities built with NaCl, one for each function (crypto_box, crypto_secretbox, etc.). Minimal non-djb code. In the interests of experimentation and learning, I prefer using small, separate utilities versus applications that do multiple jobs.
I would be interested in an "expert" opinion on my experiments with these utilities but crypto is such a devisive topic. Though they may be initiated as sensible, honest questions, online discussions quickly turn toward dogma supporting status quo, mindless memes, subtle insults and are sometimes derailed into the realm of absurdity. I would post an example of the usage for comment, but I am not interested in being chastised by the HN peanut gallery. It is just intellectual experimentation, nothing more.
IMO, as a general principle not limited to crypto, there is nothing wrong with "custom" anything if it has passed the same QA tests as the "mass-produced" version. Sometimes in fact custom is higher quality than mass-produced. Popularity does not always signify higher quality. Perhaps nowhere is this more evident than in the world of software.
IMO, a "naclwrap" program would be very useful, even in a "TLS world". Like stunnel but for nacl. Whether "everyone" would use it is an interesting question but ultimately not something I care about.