Interesting. I looked at the level and yes, I guess nuke likely can be viable solution. But it seems pretty clear to me they intended non-nuke solutions instead, and after a quick play I don't feel it requires much precision either. Once you work out a good location to assign the first bomber, you can basically just assign the next few bombers at the exact same location, leaving the release rate at the initial value. After around 4-5 bombers, the falls on the right will become safe and victory is just one blocker away. The same low save requirement that makes nuke solution feasible, also makes it pretty forgiving using regular bombers.
In contrast, the Xmas level I alluded to, really does force you to solve by nuking, as you're given practically no skills whatsoever to do anything different.
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Back to topic. I guess the two main decision points are:
1) Per Simon's proposal #5, we could change the discussion instead to one about culling nuke solutions, then it wouldn't matter at least solution-wise how neutrals behave wrt nuking. Perhaps worth a separate discussion topic, though I also suspect you'd rather not hold up release of neutrals on that.
2) If nuke solutions are to stay, then how much or little does nuke affect neutrals? On one extreme, they have no effect whatsoever, and maybe the level will truly never end automatically (user must abort the level) as long as there are neutrals remaining. On the other extreme, they behave completely identically to non-neutrals when it comes to nuke, ohnoing and taking out terrain no different from everyone else. And a few variations in between, where the neutrals are nukable, but behaves in less exploitable ways.
We could certainly take a narrower view on what "neutrality" means, and consider it as only prohibiting regular skill assignments. Others may take a slightly broader view and consider it as disallowing all "direct influence" on a neutral, leaving only indirect influence via environmental changes as the way to work with neutrals. The release rate is an interesting gray area where you could read it either way: in one sense it does provide fairly direct control over the timing of when each lemming comes out; at the same time, you can argue that you are only controlling the entrances, and the entrances in turn affect the timing of when lemmings come out.
Having nuke potentially abruptly end the level when only neutrals are left, might be okay if you educate users to expect that beforehand. For example, maybe whenever the game detects only neutrals are left (for any reasons), it could pop up or display some message notifying the player to that fact, and explain that they need to either ESC to quit the level directly, or they can try nuking and we will basically also treat it like an ESC.