After some discussion at #bitcoin-wizards (freenode IRC) with Aviv Zohar and several Bitcoin devs, it seems to me that there is an advantage to the current Bitcoin rule for selecting the best chain, over the proposed rule in this new paper.
First note that there is ongoing research by Bitcoin devs to enable lite nodes verify whether txns are valid (
link1,
link2,
link3), which may also allow us to remove the checkpoints in the client because new nodes can be bootstrapped without having to verify the signatures in the entire history, hence the Bitcoin system will be more trust-free.
Consider an attacker who creates many difficulty-1 orphans that extend the genesis block (which requires relatively low PoW effort) and thereby DoS-attacks the other nodes by bloating their local copy of the blockchain with these many orphans. Note that headers-first sync will mitigate this attack somewhat, because the nodes will only fetch and keep the headers of the orphans, but it wouldn't fully mitigate this attack. Right now, Bitcoin is protected from this attack because of the checkpoints, as clients will reject orphans at genesis because of the later checkpoints.
If the checkpoints are removed, I think that Bitcoin can still have anti-DoS mechanisms against this kind of an attack. For example, the most naive anti-DoS protection would be for the node to have some quota and not accept more than certain amount of forks that extend an (old) block, with small risk that it may need to request those rejected blocks later from peers, and waste communication.
So, under the assumption that eliminating checkpoints to have a zero-trust system is a worthy goal, the question is whether we can have anti-DoS protection with the proposed rule for best chain selection of this new paper. Depending on how exactly the nodes will reject blocks that are suspected to be attack-driven, I think that there is a danger that it could cause netsplits and that the network won't re-converge. Even if the network will indeed be convergent, the communication complexity could be significantly greater, as nodes will frequently need to prove to other nodes (who rejected or deleted blocks due to anti-DoS protection) that they have a subtree with a bigger weight?
I think that there are pros/cons to this new proposed rule versus the Bitcoin rule (the complexity needed for lite nodes is probably another disadvantage, and of course there are also significant advantages as discussed in the paper). At this particular moment in time I'd feel more secure to exchange my fiat money for bitcoins than for a cryptocoin that implements the newly proposed chain selection rule
But I'm of course open the possibility that the new rule will lead to a system that's more secure overall.