1) charging miners for the cost of network transfer
2) charging transaction creators for the cost of network storage (if their UXTOs are not spent / not feasibly spendable)
3) removing the blocksize limit altogether.
2) can be addressed by a 1 satoshi per day fee on all outputs less than 5460 satoshi UXTOs. Within a day this will prune all the 1 satoshi spam from the blockchain. The 5460 satoshi threshold can be halved every block cycle until eventually this fee no longer applies.