Trying to keep the game alive, are you?
You plan to make every ship unique, yes?
Simple. Make progress easier and faster. Perhaps let players upgrade some of their standard ships like they can upgrade the Ellidium ones. Pick a few special ones for starters, like the Phoenix, Reaper or Bear (Who the hell needs 3 different tacklers on one rank anyway?) Change the way the ship tree is handled with the old factions, simplify it if you must. Let the players with greater skill and knowledge win and not those who either paid up or spent ridiculous amount of time grinding away. First try to satisfy the veterans, who, like myself, have been playing for a long time and don’t have the time to play for hours every day just to complete silly equipment and rank limited tasks anymore. Especially while there are also other parts of the game to focus on, like the Sector Conquest. If you can, keep the veterans in and perhaps make some of them speak better of the game. Then try to attract more new players and offer them something more than a vision of grinding for hundreds of hours to get something cool, only to have it either nerfed or rendered obsolete by the next new thing, for which you yet again need to grind for hours and hours. Or to fork over a lot of money.
Only 3 MM levels could be acceptable, but not in the current state of the game. And not with the passive bonuses. At the lowest level, the starter r1 ships can hardly compete against r5, even with bonuses. And since some of the PvP battles there are made into co-op for difficulty and low player count reasons, you should put more effort into making it a proper entry-level part of the game. Perhaps make a set of quests or create a couple of exclusive PvE/tutorial missions to better familiarize new players with the mechanics of the game. And only after that, let them join the intermediate level of r6-r10. With easier and faster progression, ranks 6 and 7 should only serve as a stepping stone for rank 8-10 gameplay. Have the players get familiar with the new stuff the next tier brings but give them no passive bonuses, only let them use implants up to rank 10. After that comes the endgame tier. Here the passive bonuses can cause the greatest chaos. R11 destroyers out tanking and out damaging r14 ones. Or things like Gargoyles and Darts with passive bonuses to damage and resistance. Again, implants up to the max rank present in battle for every ship, but no passive bonuses. If you could make some, if not all, of the ships upgradeable, those players who would want to compete could either buy the max rank ships or upgrade the unique ones. Bringing up some of the ships to r15 through upgrades could also make some of the DLCs more desirable to players.