Yeah, playing with this mod in 0.9 would be nice. I remember tearing apart entire fleets in a fully upgraded perfect Shadow Cartel Medusa, although that is also one of the main annoyances I had with this mod - your ships at some point become way too OP, and there is no option to limit your power level or raise that of the opponents to the point where the game keeps being fun (random upgrades on AI ships rarely made a powerful enough combination of upgrade lvls/ship quality/officer quality/ship type, and even then they were basically alone against all your fleet). If I could (I wish I could), I'd change some things around to make it more balanced.
First of all, add the ability to improve the ship quality.
Before, it was a long and frustrating hunt for that perfect ship, wasting millions on Paragons and Medusas to get that one with Q>1.4 and forget the rest in the Omnifactory hangar. Now it will be a hunt for the blueprint, so you can order a hundred Paragons to get on average one with Q=1.5 and, well, forget the rest in the hangar (or sell for hardly 10% of the cost). I think we can skip a step and just make the cost of upgrading a ship from Q=0.5 to Q=1.5 as 100 times the cost of manufacturing it, spread it across 20 levels and then skew the cost to make lower levels cheaper, and higher - costlier. About 10-20% of the total cost should get you from Q=0.5 to Q=1, to create the incentive to upgrade bad quality ships instead of waiting for the perfect one and ignoring everything below Q=1.25.
Second, change the ability to upgrade categories with the ability to upgrade each value at a time.
Like Taurus84 said, it will add more customisation options, but if you still get all the upgrades eventually, there is no point in more detail, the effect would be the same. What I think we can do is combine categories and individual upgrades so that the amount of upgrades per category is limited, thus creating actual choice. For example, if you want to upgrade durability of a frigate, you have 5 values to choose from - hullpoints, armor, weapon health, engine health and EMP resist - with 10 levels max in each, so in total you have 50 levels in that category. If you limit that maximum to, for example, 50%, you'll have only 25 levels to spend and now will have to choose what is more important for that particular ship. This will need some balancing of those categories for sure (I'd say swap EMP resist and shield efficiency), and the option to change the limit for max upgrades , so you can choose to play with 100% upgraded OP ships or try some precise optimisation with 30%.
Thinking about it, I see one problem that system will definitely struggle with, that same problem the skill tree struggled in older versions of Starsector - some options are just better than others. Hardly any ship will pass upgrading weapon damage, or speed, or flux dissipation, and only then the actual customisation begins, which sabotages the whole reason of remaking the upgrade system. I suppose the way to alleviate the problem would be to remove the best options for each ship from each category (I'd say hullpoints, weapon damage, maintenance, max speed and flux dissipation) and tie their effect to the max level of upgrades in categories themselves. For example, if you have 50% of max levels in, say, mobility, you'll get 50% of max speed upgrade effect, and each subsequent upgrade in the category will improve it's effect automatically. This way it also will work regardless of how many upgrades you prefer, 100% or 50% or even 10%.
Third, some changes to the way AI ships are affected by the mod may be needed.
From what I remember, AI ships got their upgrades randomly, with no correlation between ship quality, officer quality or the type of the ship itself. Higher level bounties had ships with more upgrades, but no guarantee they will land somewhere it will matter, thus not making any expencive bounty all that stronger. If there is some way to tie upgrade progression to the difficulty of the encountered fleet (or even make it dependent on fraction and their industrial capabilities), I'd look into it. Adding some extremely expencive bounties against fully decked out fleets can make endgame very fun.
As a quality of life improvement, this mod definitely need the ability to see the quality level of the ship before adding it to your fleet. It was very annoying to save-reload only to measure whether a ship is worth taking or not.