Isn't it only pay-to-win if people can purchase things from the game's store which they cannot acquire through grinding in-game? if the developer was to only "seed" the game initially with mods and ships but then turn over the economy to the players through an uncapped tier based crafting system then everything in the game has to be created by the players. As in MK1, MK2, MK3 shields for your ship (for example).

Perhaps dig into CSC. The concept of that MMO was great but unfortunately the company decided to let the game go.