All these retro looking ships are brand new. They are designed and been build in STO time, with new technology, engines etc. The devs have said that many times before, nobody is using 140 year old ships in this timeline.
Second of all that T5 BoP retrofit is technically a prototype it is mirrored BoP of General Chang BoP but designed in STO time brand spanking new, with state of the art technology etc. CBS is ok with that probably because it is based on star trek canon and it makes sense. I've seen all star trek canon and never seen T1 Miranda been similar to what Klingons did to their BoP. this is just an example.
That T5 BoP retrofit is tricky ship to fly and you would do much better using T4 BoP than T5 retrofit BoP. I fly it because I like the challenge and because it is iconic Klingon ship.
I don't like the idea of scaling ships but I would settle for some kind of MOD that T1,T2,T3 ships could use to give them slightly better chance at higher levels. This MOD that you could put into special slot would slightly reduce the damage but original ship would still have the same HP and weapon loadout. Also the cost of that MOD would have to be like 1600CP. First MOD you could equip it at level T2 and it would last till level T3 than at T3 you would need to buy new mod for 1600CP and it would last for the next 2 levels, T4, T5.
So in conclusion T1,T2,T3 would have a little better chance staying alive with that MOD than without it. But the original T1,T2,T3 ship would not be changed in any way only slight reduction in damage will be made when using that MOD.
Anyway that MOD idea would probably work with Cryptic and CBS but to be honest I would not pay for that mod maybe someday but unlikely. I would rather buy new ships and have more fun with them.
And what would need changing if we had a scaled system? We already have ships that partially scale (Shuttles) so the tech is there to make it happen. I'm not seeing your objection based on "needing to change so many things" because that's just not the case.
We have scaled system for shuttles because Shuttles dont take much part of gameplay, there is only one mission were you have to use them.
The system for a entirely scaled system would mean having to change thing so they would scale to your character rank, potentially the BO consoles ranks could be tied to your rank but some things really have to be set in stone, a ship weapon slots would be one (since they had to be canonical) so there would a limit to how they can "scale".
I am not saying the idea does not have merits as I agree with some points but not on other but consider this, if this goes to the C-Store and we get a reworking of Space that makes this "scaled" ships obsolete what you think would happen?
This is something that if its done by C-Store that means you are locking the Space system as it is, they cannot really significant alter it if it makes C-Store items obsolete, getting these changes by C-Store means you get your scaled ships ... at the expense of the current Ship and Space system being locked.
So if they give you a ship like this you pay for it once and really whats the point to use C-Store after that? There is no point. I get my ship and fly it all my career without spending any more $$ on C-STORE. Thats not what they want you to do. They would rather give you many more ships, extra ship slots, all kind of other bits and pieces and put it all on C-STORE. That way instead of paying 1200-2500 you will put about 10.000CPs in their pocket during your career one one charcter.
Simple fix for this problem. Make it unlockable on a per character basis.
I got all excited about this, but then saw the no to tier 1 ships. A very well thought out suggestion though, and it would be nice to fly some of those ships but I would say most would prefer to take some of the ships from the shows through the game using this method. The intrepid, galaxy and sovereign are already up there in the high tiers along with the excelsior and the nebula. I would only really be interested in flying the NX class, TOS Connie and TMP Connie with this kind of upgrade. I don't PvP so it would just be to play STO in my style of Trek, I ilke to RP... so shoot me . To close this comment, I would say before some people come in and start saying "but the NX/TOS Connie are so old! They belong in a museum!" I fly the D'Kyr with my Vulcan Science officer and all Vulcan crew. That's a VA ship, which for the record is even older that the NX class... go figure.
As an supplemental suggestion to the OP's... IF CBS won't allow for the use of the canon ships to be used in such a manor, is it (would it) be possible to use the old Perpetual ships that Cryptic owns?
Buy that ship at Lt. Commander as a per character unlock. Then apply the progression as listed in the OP.
No, people couldn't keep their Nova (damn shame if you ask me,) but it's not violating the established story-line ships, and there are NUMEROUS ships that perpetual had designed that could (would) be awesome to get in game, IMHO.