NXT blockchain pruning does not even have the concept yet. It won't be easy as some claims to be. If blockchain pruning can be done at will, why do bitcoin not have one already ? So I would say do that first before attempting ping pong messaging.
This is not totally true. NXT has a good concept around removing everything but the blockchain itself. Transactions, messages and trade logs are stored in a way, that entries older than XXX days can be pruned. There is nothing decided yet, about the rules ect, but it is not so far away as you say.
As for bootstrapping, that is basically ready for BTC. Not sure why you say otherwise. It is not implemented because it is a nontrivial change, that is not needed 100%. That's why!