I have a bit of a controversial opinion; I don't mind the milestones not being retroactive. I understand the intention behind this; We've been leveling up our pirates, now it's time to level up our ships. Yes, the numbers are a bit ridiculous, but I'm sure they will be adjusted at some point to be less so, based on the sheer amount of feedback regarding it.
I also understand locking all the customizations so far behind these milestones. It's a brand new system, and they want to encourage players to get out there and do this big new thing they've added. There's a case to be made about it all just being things we've done before, but it makes the assumption that new milestones are never going to be a thing, which I do not think will be what ends up happening.
I will, however, say this: I also understand where a lot of long-time players are coming from. It's like climbing a huge mountain when trying to get somewhere- Then seeing that there's another, bigger mountain left to go. Plus, new players will be able to just climb both mountains simultaneously, so like- Ouch. Stings the pride, just a bit.
But, this is not an unsolvable issue! I think, it would be nice to see some trinkets/trophies/interior decorations retroactively added to commendations that do not currently have a reward. Not the same things you can get through milestones, mind you- Completely different ones, or at very most, reskins. Y'know- Give a point to doing both. There's already one example of this with the Shrouded Ghost trophy. Honestly, it doesn't even need to always be a physical object on the ship, Ship Titles would do just fine as well.
That said, I can see how it would be a strain on the art department, making new customization options for two seperate progression systems. Or, perhaps rare just wants to double down on milestones, which-y'know, it's their game, they're allowed to do so. It still doesn't leave us without options.
So, as the ultimate form of compromise, I'll pitch this:
A new milestones category: The Commended. Each category of commendations is listed as a new milestone; for example-
Reaper's bones commendations unlocked:
Hunter's call commendations unlocked:
Sunken kingdom commendations unlocked:
Etc. Etc.
Due to the nature of commendations, this one would need to be retroactive [as they can't be unlocked again], but it'd be the only one that is. That way, veteran players get some additional recognition of their history, milestones no longer feel like a reset, and new players get more incentive to play through both methods of progression.
Once again, I understand both sides of the argument; I'm just attempting to offer up some solutions I think both sides could agree on.
EDIT: I'd also like to open up the floor to anyone else who may have their own opinions on constructive ways to address the situation that aren't just "Make milestones retroactive!" Because we've heard that plenty.