I think the Arrival Checkpoint works, as well, but you might want to add a few crowbars inside the arrival shuttle, so that people can always get to the oxygen tanks, and thus, break the window.
I'm pretty sure that the Arrival shuttle can't lose power so the airlocks leading to the oxygen tanks can always be accessed, plus I remember the chaos that happened when I tried putting oxy closets in the shuttle itself last time. I'll add a couple toolboxes in the rooms
with the closets so that one could break out should the airlocks leading
out lock up, but unless the AI or a hacker locks them themselves I'd rather leave the dangerous objects OUT of the starting area.
Maybe I could rig up a switch to open those doors that requires an ID card?
Vats are great for refueling tanks and even igniting the engine. A few somewhere would be cool, plus, we have them, might as well use them. 
Of course, do you want me to hook them up to the engine itself or keep them to the side?
If you could somewhere squeeze in a small room, for lawyers and their clients to talk in, with privacy, would be very nice. I don't know where, though, room around the courtroom is scarce.
I could convert that nook in the Bridge above the courtroom to something like that, it's just filling space as-is.
I agree with the idea of a crowbar on the shuttle. I'd say perhaps have a tools locker on either side of the front of the shuttle with some absolute basics... though I don't imagine it would be too difficult to rig some doors, even lockers, to open under emergency conditions.
Remember, I'm a mapper, not a programmer. While I have a bit of general understanding of programming languages and could maybe hack out a way to do things, it's entirely theoretical for me. I'll keep your suggestions in mind, though, and see what I could/couldn't do easily.
Such as Airlocks to an outside, grated area, that can be walked across to get to another part of the station, that will likely hurt you, but in desperate times, will be nessescary.
I can add some walkable tiles and airlocks around the station's exterior, but grated or not you're gonna die without an EVA suit.
Or maybe a way to enter the engine block, to get to certain parts of the station, which is INCREDUBLY dangerous, but again, sometimes nessescary.
Wait, the engine itself? There's maintenance corridors in the middle which should allow some sneaking and skullduggery, but I can't see ANY feasible reason to allow access INTO the engine other than the places that allow it already.
We also need to re-add air-bridges, they would be good to be able to be deployed by a person who has taken the dangerous route, so the rest of the crew can move through unhindered.
Unfortunately, I have no idea how the airbridge works, and haven't even SEEN it outside of the classic station. I could use them in place of the stationary supply/prison shuttle walkways, but that's still going to have to go into the "maybe" pile.
Could the AI have more vaccum protecting it's back?.
I'd definitely consider it, but unfortunately the station already takes up most of the y-axis of a 150x150 tile map, so I'd have to either cut into the already-cramped Atmos room, or into the escape shuttle. The only way I think I could do it is by shrinking the AI Upload room unless I can resize a map.
One quick thing about Atmos. Give it some way to vent siphons to space please. If we get the ability to release specific gasses from them, great, we can sort them out, but short of that, the only way to really empty a green siphon full of plasma and CO2 is to either use it, or drag it to an external airlock, which Atmos techs don't have access to. Nothing much, just a 3x3 room with a blastdoor/grate combo like in the engine lighting area leading to a square or three of vacuum.
I could probably see about putting a couple pipes that vent out into space that you could hook up a siphon to, but Atmos is pretty cramped as-is, so It might have to be in the maintenance corridors if anything.
Also, you may want to remove the atmos pipes leading to the arrival shuttle entryway thing and replace them with those shuttle filters. Or maybe just leave them, and add a few of those immobile filters. That would help prevent random griefing of the arrival shuttle by filling it with CO2, but still allow a determined atmos traitor to disable the shuttle.
I was looking for a reason to use the stationary siphons. I'll put a couple there.
This should be possible with what's already in the game. The very original map(Before goonstation and all the offshoots) had a brig with secure doors you opened via putting your ID into a panel where you had the options to open inner brig, open outer brig, emergency open both doors, or emergency close both doors.
I was thinking of a couple regular buttons for those doors (heck, if someone can break into that room, let them open the doors themselves) but that DOES give me an idea for the oxygen tanks/equipment closets problem with the shuttle.
Engineering needs to either have those vats from the more recent version, or a way to give the engine more of a good boost. Given the limitations of piping flow(You have 5 input canisters using the same pipe, at most maybe 2 will be releasing due to pipe capacity), there may need to be a better way to load the engine before hand. Doing it all by dragging into the chamber itself is going to take quite a lot of time given its design.(Not to mention multiple engineers getting in each other's way when trying to load it)
Unfortunately I did make the engine loading hall a little cramped, and I didn't even THINK about pipe capacity at the time. I could see about modifying their capacity maybe, and do a bit of rearranging, and possibly splitting some of the pipes to go to a separate set of vents, but I'll see what I can do. Incidentally, is that "at most maybe 2" referring to two per pipeline, or two total?
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