Looking back at the release version of the game... your science ships would randomly explode when they fail to survey an anomaly, they would meet certain death if they happened to jump into a system with a roaming creature near them, and those space aliens wouldn't care much about whether that system they're moving towards is owned by a player and happily eat through those mining stations that you had just set up. That sort of stuff... can be annoying, but to be honest, it's also part of what creates memorable moments.
They've already made the universe very tame... no anomaly failures, aliens avoid player territory if they can, there are fewer neutral aliens than there have ever been, and most hostile spawns are restricted to non-choke point systems... and all of those might be sensible decisions, but where do we draw the line? Do we really need protection against RNG that might give you a hard time every once in a while? The more rules we have to prevent "bad outcomes", the more same-y every match feels.
In case of the Spectral Wraith, it can only spawn on a pulsar, gives a warning when you survey that pulsar, is very easy to counter and even has a color-coding mechanic that you might or might not be able to abuse. It's also very obvious when it will spawn, which is basically right after the mid-game pulse, so really, you know when you need to have finished your preparations.
The Wraith is certainly capable of causing massive problems if you don't know how to react, or have never met it and as a result don't even know that you have to react before it's too late, but overall it's not at all a situation where you're left with no options.
