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I'm not following your thought process at all here. Why would you want to not notice it? It's basically the exact same engine core as in vanilla, but higher-poly. We're not turning it into the Enterprise warp core here.
tweaks to the architecture have been a thing for a very long time.
..other times it's just so different that your memory flags it when you get there and you have to stop being the soldier in ss2 for a moment and pull yourself out of that to say... "oh yeah this is where they updated the engine core... huh.." and then go back to playing again. I just don't want that to happen while playing the game
The insides of the nacelles would be exactly the wrong place to visualize their state, since players have to go out of their way to see it. The ideal setup for this sort of thing is something you can't miss, like how the central engine core is set up. Players always see that it's dark on their way in, and lit up on their way out.Unfortunately the nacelles don't have much in the way of external affordances for indicating their state. There's an ambient sound in the nacelles that could be made to only play after activation, but visually... I dunno.
"oh yeah this is where they updated the engine core... huh.." and then go back to playing again. I just don't want that to happen while playing the game.
I would recommend adding some big "Nacelle A: Offline" and "Nacelle B: Offline" displays to the main engine core area on the ground level where you walk in
The nacelles are a bit of a wasted gameplay opportunity if you think about it. All you have to do is enter each nacelle, head directly left or right to reach the control room, click the big button, then leave. Irrational could have easily mixed things up by damaging or throwing debris on the walkways, forcing players to figure out a path to the control room.
I don't know if it would break the AI pathing, though.
It absolutely would. If the pathfinding database tells an AI it has a clear path, it will walk into a solid object forever trying to follow that path.