Thanks for writing this up @ari!..I’m strongly in favor of the main thrust of this proposal, but echo the sentiment that others have expressed that we should seek to remove the requirement for positive query fees and reliance on the Gateway.
To add some color to the discussion above, this proposal isn’t so much about query fees not being enough of an incentive, but rather making the fixed costs of serving queries as close to zero as possible. This makes it economically rational to serve any positive amount of queries, and thus makes rational self-interested Indexers (all you altruists aside 
) more responsive to query fees, which we should expect to result in higher quality of service for the network.
In terms of the effects on smaller Indexers, it’s true that aggregate costs to Indexers would go up if Indexers didn’t change their behavior in response to the protocol change, but I find it more likely, as @ellipfra noted above that we would see fewer Indexers per subgraph. This prediction is described by \text{Eq }(20) from Prysm Group’s PoI Spoofing Analysis which relates fixed costs to # of unique Indexers as follows:
\text{# of unique Indexers} \propto\sqrt{\frac{\text{indexing rewards}}{\text{query fixed costs}+\text{indexing fixed costs}}}
So while it’s true that this should increase the fixed costs per Indexer allocation, I wouldn’t necessarily expect the overall costs to Indexers to increase as Indexers adjust their number of allocations accordingly.
As @ellipfra noted, fewer Indexers on a subgraph is undesirable, all other things being equal. However, in the context of this proposal, I believe that it is better to have fewer Indexers on a subgraph that are all fully responsive to the query fee incentives, rather than more Indexers per subgraph that are largely indifferent to the query fee incentive, given the large step up in fixed costs to collect fees for even a single query.