So I played through 5 runs with your changes, and I have got to say it was really fun!
I really liked how you addressed my biggest gripe with CE - that being the boatload of useless weapons and augments - by not just buffing them into a usable state with a reasonable cost, but most ingeniously, addressing many of the utility augments that weren't worth it in base CE due to them using up one of your precious 3 augment slots, by packaging them together into augments that are multi-functional, and upping the combined cost.
This of course makes the game easier, due to increasing the chances that you will find reasonable additions to your loadout in stores, but is also counterbalanced due to higher upgrade costs notably in Shields and Engines. 100 Scrap for Level 2 Shields is brutal! You'll get the scrap back later on due to more space in your hold that is freed up for dealing with Trade Goods.
The addition of descriptions of which sector each Trade Good will sell well, in both the store and in the augment descriptions themselves were also a good addition. Frankly, I was already cheating by looking them up in the .xml files anyway
so being able to know them directly in-game was cool.
My only gripe is that Level 6 and 8 Engines are sooo expensive as to almost never be worth it to go past Level 5. Level 6 costs as much as Hacking or the entire 4th shield bubble!
I understand that they give you an additional beacon per sector (I really liked the staggered upgraded costs btw) - it's just I can never seem to afford it. From my experience, I usually only get enough spare scrap to get Level 6 once I am at Sector 6/7, but by that point you only get 0/1 extra jumps out of the upgrade, so you're probably better off buying something else. That said, you usually never have enough scrap to spare in the base game anyway, so I guess it works enough to prevent exploits!
But anyways it's a great mod! It's good enough to release it as a standalone along the lines of Captain's Remix, I reckon, if it can be updated to FTL 1.6!! Its definitely how I will be playing CE from now onwards
Edit: So I went ahead to make 2 small edits to it - simply to remove the buggy hangar animations, as well as bringing the costs of Artillery down to 80, which is what CE is using at the moment. No idea how to fix the tooltips yet though.FTL CE ZHO Mod