I see. I really disliked Kojima using nanomachines as not only a copout plot device, but also as a means to retroactively explain/ruin the awesome villains he built up in past games. It didn't really matter how in depth he went into their inner workings, it still felt insanely cheap and unnecessary. Him doing the exact same thing in MGSV with the parasites was unbelievable.
I agree for the most part. I actually enjoyed MGS4's story and it at least felt complete and cathartic when finishing it, even though I didn't appreciate certain aspects (like the retcons, nanomachines unnecessarily explaining away powers and used as a copout for other things). At the end of the day, despite it's plot failings and questionable gameplay structure, it's still the last Kojima game that still felt like MGS to me.