I have yet to find the perfect shoe, it is usually a compromise on one thing or another to get something else. I think it is important to find a shoe that is right for you and suit that shoe to the appropriate applications. Thru hiking is a interesting issue as the conditions experienced are usually varied.
Thru hiking in minimalist foot wear in my experience will result in instances of appropriate and favorable usage, even pleasurable at times. But it will also result in instances of misuse with detrimental results, overly rocky/sharp terrain or man made surfaces. While it is entirely doable in those situations, it is a hindrance.
To mitigate the downsides of minimalist foot wear I see two possible directions to go in, one carry another pair of shoes for trail/camp/town. This could be minimalist trail runner or something like crocks. Crocks would be good in town and camp while trail shoes allow you to make it work in all three areas, trail, camp and town. Which leads to the second option and that is to forget about carrying two options of foot wear and find a shoe that maximizes what is good about minimalist foot wear, while also allowing the completion of a long distance hike and the various conditions experienced with relative comfort and safety.
Which is basically asking for a piece of foot wear, that is a middle of the road type deal that is good enough for most conditions.
For me that would be a
1.zero drop shoe (3-4mm drop provides a nice middle ground)
2.Toe Box – shape it like a real foot, not just a wide foot box but one that does not push the top outside toes inward.
3. adequate lacing and structure to provide secure fit Top down and front to back.
4. adequate drainage
5. adequate construction and materials to prevent wear out and popped seams, typical failure example: outside of the foot side wall blow outs. Or the seam integrating shoe cover and bottom.
6. minimal height off the ground. minimizing roll over and ankle twist.
7. minimal forefoot rock protection, (all-ah NB MT100's) 1mm rock plate
Vibrams are 4mm eva foam and 4mm rubber.
8. I would look for something in the 10mm range of durable eva foam and 5mm rubber and something like 2-3mm longer traction spikes to give a bit more grip and cushion that last longer. 15 to 20mm total height off the ground vs 8mm of the vibrams.
9. Lightweight durable quick drying material
10. I prefer brown shoes, so that would be a nice touch.
Every ones middle ground will be different depending on the user and changing conditions.