I think that at least one checkpoint should be included.  The assumption is that no 50k re-orgs will happen, and that assumption should be directly checked.

Checkpointing only needs to happen during the headers-first part of the download.

If the block at the BIP-65 height is checkpointed, then the comparisons for the other ones are automatically correct.  They are unnecessary, since the checkpoint protects all earlier block, but many people would like to be able to verify the legacy chain.

This makes the change a soft-fork rather than a hard fork.  Chains that don't go through the checkpoint are rejected but no new chains are allowed.