Okay so, why is it that going from Loop 1 to Loop 2 makes the difficulty feel like it ramps up exponentially without much really changing?
Like, I just started my second loop after handily defeating the first loop, but now I got to day 15 with virtually no progress being made, which is usually my marker to tell me that I am doing something horribly wrong and need to start the whole loop over again.
Here's the saves in case anyone is willing to give me a helping hand.
So just something I see right out of the gate, you're training your Forsaken Shadow for EXPO when you should be training her for ANTI since she has Consuming Harvester for her Harvester position, which gives her a permanent stacking modifier that boosts her TICK damage every time she does a T4 CON Break. Also, your Forsaken are doing 3 damage types instead of 2, if you handily beat the first loop you should've had plenty of time to better train your Forsaken (which you didn't, handily beating the first loop is finishing the loop before Day 50 with Imago Quickening), yet it seems like the only training they've received is from the passive training plan training. Granted this is just an observation and advice for the long term, you cant really fix your Forsaken quick enough for them to be relevant for Loop 2.
Now for the things that would actually help you, what is your battle strategy here? Cause while Rogue is going to be a pain to break, I downloaded your save and started Loop 2 from Day 1 and played up to Day 15 and was able to get all T1 Breaks and T2 MOR Break on Decree, a T2 INN Break on Vanguard, T1 CON and DIG Breaks on Rogue, and have all of them producing 2 EE a day. When I played your save I got all the upgrades done and fielded my first 4-2 Commander (4 Capture Duration and 2 Capture Attempts) on Day 12 where I got all the Decree Breaks, Day 13 I fielded that same commander and got the Vanguard Breaks, Day 14 I did it again and got the Rogue Breaks, leaving me with all those breaks, 6 total daily EE gen, and 15 EE to spend on whatever I want going into Day 15.
In order of priority focus Decree > Vanguard > Rogue, as Decree will be the easiest to break, Vanguard second easiest, while Rogue is going to a pain with her extreme PLEA resistance making bigger surrounds very hard to get on her.
Oh also another
really important piece of advice
do not use Inevitability, it is a newb trap. Inevitability is worthless in the early Days as you need every EE you can get, losing 1 EE a day will set you back massively, the goal of the early days is to rush 4-2 Commanders as soon as possible and the EE drain Inevitability makes using it slower than not having an item at all. In the save file you posted your latest save is Day 13 where you do not have all the 2 cost upgrades and have Inevitability activated, that Inevitability draining your EE is why you accomplish nothing by Day 15. It's also meh in the middle and late Days as by then pretty much all your Trauma damage is coming from Surround's Circumstance attacks,
not you directly attacking. Inevitability is the one starting item that is almost universally worthless, even Inferno Pepper, the second worst starting item, can at least be argued to be at least a little useful as free 1 cost Commanders can slightly speed up getting to 4-2 commanders, and getting a 1 EE refund on 4-2 commanders can slightly speed up getting through upgrades. Remember, on Day 1 you're allowed you swap your starter item with any of the other starter items, so if you get Inevitability do that swap to literally
any other item.
tl;dr, the difficulty didn't massively ramp up, you've just been playing poorly and the small amount of trauma resolution in Loop 2 is just enough to stop you from walking through everything unlike Loop 1. Also the Chosen in Loop 2 might just have a more difficult layout of Vulnerabilities than Loop 1, like Rogue being a general pain to break in isolation.