As for your idea on the stealth ship, I'm just going to say that you're crossing into paranoia with that. I know not to underestimate the Leviathans, but I really think you're overestimating them.
How am I overestimating the Leviathans by referencing a technology that's becoming more and more common? First it was just the Normandy, now the quarians suspiciously have it for some reason, and you know Cerberus isn't going to only outfit one ship with it..
The ships are there, for the thralls' taking.
Also, the observation isn't so much to cover the entire planet. It's more to keep people out. You're making just as many, if not more assumptions, as me. The only point I'd take in any kind of serious contention is the idea that more science teams might be enthralled. Also, preventing organic stupidity is easy. Exploit their greed. I change something. Instead of marking the system as a military reserve, I'd mark it as a scouted system that was surveyed and found to have nothing in the way of valuable resources or opportunity. It'll get ignored, and it's in a region of space that is already fairly remote. No ones going to bother with it if there's nothing there.
I was referring more to thralls sneaking in and out and the equivalent of perimeter guards being sloppy than randoms just stumbling on the planet. Randoms are irrelevant. Thralls flying under the radar you can't prevent.
As I said, I really think you're overestimating their capabilities in an effort to be 'crazy prepared'. To be frank, it comes off as extremely unrealistic and paranoid. You're putting all these what-if's together and then ascribing them to the Leviathans, and relying on a 'we don't know that they can't' ideal to justify it.
Wrong. We know that they can. Yes, the stuff about being able to leave on their own power or being able to fling the orbs into space, that's speculation. I wouldn't base an argument on that. But using thralls as sleepers and using subterfuge to sneak past your little blockade? Hell that's puny human stuff. Of course they can do it.
It's not paranoid at all. My point is to show you can't possibly bottle them up. This isn't a game preserve. You can't just install the space version of a little electric fence around it with "No Trespassing" signs and expect that will work.
Leviathans were the apex race of the galaxy. Their arrogance knows no bounds. Everything in their dialogue indicates all they care about is thralls and if given the chance they would rise up and take over the galaxy again. They were only taken down and kept in check by the Reapers. And that wasn't through containment. That was through massive destruction and genocide. Without the Reapers around, the Leviathans must be destroyed. Unless you want your newly freed galaxy to scrub their scales for the rest of their lives.
And I honestly believe they didn't plan for that eventuality. I don't believe the Leviathans are the 'crazy prepared' species you're making them out to be. I think that they'd start thinking about it once Shepard brings it to their attention, but I think they have too many behavioral issues to plan for the eventuality of being discovered. I think we'll be fine as long as no new thralls come to the planet. In fact, with all the Reaper tech scattered across the galaxy post-destroy, we'll have plenty of things waiting for them. In fact, you'd probably be able to mitigate the stealth ship with the Reaper sensors.
Are you kidding me? This is the species that wiped all traces of themselves from the galaxy once the Reapers have left. Did you not notice how hard they were trying to stay hidden? That game is up. They know it's up. Only an idiot would fail to realize that it's up. They aren't very confident in us puny organics winning the war so of course they're going to plan for worst case. That's not being "crazy prepared" or paranoid. That's just common sense and not being a dumbass. Yes they're arrogant. But before that arrogance comes survival. And the Leviathans didn't survive untold milennia just to die because some uppity human couldn't leave well enough alone.