okay. i finished this. unfortunately, it appears that those are the only main items you can get early (ignoring some random collectables)
Exhaustive play-by-play rundown
No sequence breaking is possible before going to Sector 2 (TRO) the first time. Access to TRO before SRX is blocked off by the nav room, as in the original. Likewise, the game still does the thing where you’re locked into the sector once you get your briefing there.
In Sector 2 you can get the power bombs early by wall-jumping. You can then continue on that route for a few rooms to get the Plasma Beam from Nettori, though I recommend getting the high jump first because jumping over that eye Core-X is a pain (and it takes a lot of hits without supers).
After that you can exit out of the TRO backdoor to the main reactor to fight Yakuza and get the Space Jump (plasma appears to multi-hit his first form but not the second). However, taking the TRO backdoor requires bomb jumping (I cheated and used frame advance). Seeing the main reactor room without vines and stuff was weird (it even makes sound!).
Both of those boss-fights are pretty grueling when done early. Boss health/damage scaling feels very aggressive in this game.
I tried going back to the main deck, but there was a creature blocking the way (this was in the original, where it forced you to go to the ship and get briefed before heading to the reactor).
It appears that you might be able to leave leave TRO without getting the high jump, but I didn’t test that.
Heading into PYR before AQA with PBs and SJ doesn’t allow access to anything more than the original game does.
You can get an early PB tank in AQA if you already have PBs. (I’m curious if its possible to lower the water without getting the speed booster.) Also, you can apparently go into a couple rooms in lower AQA early, but all the paths are blocked off (I’m assuming the original game was like this too).
You can get the Wide Beam by heading to the main boiler right after unlocking the security hatches in PYR. This entails doing a nice run through a series of heated rooms. The possessed scientist is just standing there at the controls. (I like the implication that he was there the entire time, just waiting for the right moment to destroy things.)
You can skip the BOX-1 fight by… just space jumping out of the room when it starts. (I love it.)
Going into ARC before NOC yields the same results as the original game: not only does the cold do continuous damage (like the heat), but it also produces knockback on a regular interval, meaning you can build up a speed booster charge to access the security room (and thus the data room). A cold run should be possible if that effect were removed.
Having power bombs for the NOC SA-X encounter is kind of funny to me. Using them to blow up the wall immediately alerts the SA-X before it even properly enters the room.
Speaking of the SA-X, I didn’t run into it in ARC. Weird.
After I got the Ice Missiles and returned to the ARC navigation room and it told me to go to ARC (because of Nightmare), I’m assuming that’s because I had already done everything between the first and third ARC visits: getting the wide beam, power bombs, space jump, plasma beam, and also saving the ani— wait a minute…
I didn’t do that…
I checked after I noticed that and it looked like the animals had already saved themselves. 
After that the game continued normally until the end, until the escape sequence where I decided to collect a missile tank, inadvertently bringing my completion percentage up to 69% (nice).
Thoughts on how this could be improved
- Remove the cold air knockback effect.
- Get rid of the event doors that lock you into areas after being briefed.
- Make screw attack blocks destroyable by power bombs (and maybe vice versa)
- This would allow access to the inter-area bridge system earlier than the end game (maybe that would be too open)
- This would make it so nothing (other than your sanity) would prevent you from fighting Ridley right after Power Bombs
- This would require extensive analysis of level design to prevent soft-locks, etc.
- Make security doors destroyable with certain weapons (I mean, if the SA-X can…)
- Make saving the animals a requirement (maybe just for a randomizer, idk).
- Normalize Core-X damage so they die after a certain number of missiles, regardless of your missile type.
I look forward to further revisions of this hack, and it being used as a base for other hacks, randomizers, etc.
