Dear Daniele,
This is a splendidly written essay and rates very highly in my opinion. Though I have a deep love for GR (it's what kindled my first interest in theoretical physics as a child), nevertheless the subject of its limitations and possible extensions must be boldly faced. I only hope that whatever replaces it will retain some of the conceptual simplicity and deep unifying principles of GR, however awful the mathematics! A few other thoughts:
1. First, I am grateful to you for alerting me to the general importance of boundary information in this context. I was not aware of the properties of matching Schwarzchild solutions across a boundary.
2. I wholeheartedly agree with your quote "Nevertheless, General Relativity has also some internal unresolved philosophical 'problems' and these are the issues we want to concentrate on here, arguing that the third category above [the desire to realize some aesthetic or philosophical principles] can provide some important insights into how a new theory of gravity should look."
3. Perhaps the most striking point, to me, at least is the following on page 4: "What happens is that, if we do not consider the improved variational principle including the boundary terms, as the one considered above, we end up with a matching with two arbitrary Schwarzschild solutions that are described by two different mass parameters which are chosen arbitrarily." This I did not know, and it seems to make the importance of your considerations unavoidable.
4. By the way, my own attempts at fundamental physics involve nonmanifold structures, but are based on principles that find their clearest present form in GR (background independence, causality, covariance). If you're interested, you might take a look at my essay here. It's admittedly speculative, but hopefully interesting.
Thanks for the great read! Take care,
Ben Dribus