I think there are a couple of interesting things in here that I’d like to address. I’m not sure if looking at things from a slightly different angle will help you at all, but I also don’t know that it wont.
Firstly, I don’t think that momentum and threat represent a balance mechanic. It’s more a case of consequences (which I’m aware can be similar) in a relatively direct, if abstract way. Using threat to buy dice isn’t necessarily the character being daring- it’s the character taking risks in order to succeed. The threat that is generated is there to represent either and escalation or the haphazard nature of the attempt.
The best way to make use of that threat is to relate any spend back to how it was generated. If they spent threat on a task to persuade someone- that person might have been persuaded, but doesn’t have to be happy about it. Spending threat to have them get their own back later makes perfect sense.
In this way, the mechanic is simply encouraging transparency over GM fiat.
On your difficulty zero check example - just don’t let/make them roll that check. If theres no consequences, then its a bit of a wasted roll anyway. D0 checks have their place, but they aren’t a catch all. It would also be very easy for you to just remove this element of the mechanic from your game, if that worked better for you.
That said, there are plenty of example situations that could be used to support how momentum is meant to work. In a d20 based game, for example, you might give a group advantage on a few checks after their leader makes a rousing speach to insipre their efforts. In 2d20 the momentum generated is a hard coded alternative, not requiring the GM to just decide to give a bonus. Again, this is adding transparency in place of fiat. Losing momentum at the end of the scene makes sure that the benefit isn’t infinite. Not every situation will be as obvious, but that is the thought process.
Finally, on your third point - this IS a joint storytelling game, so narative control is shared. There are always extreme examples of how people can abuse this sharing of control, but there is also a lot of benefit to that method. Again, as a counterpoint - the intention isn’t for the players to simply spend momentum to remove complications in that way, at least not purely from a momentum spend. Thats the other half of the collaborative nature- its a conversation between everyone in the group (GM included), and you’re all trying to tell a fun story that makes sense.
From the sounds of things, i get the feeling that you might have some luck just from tightening control over how threat and momentum mechanics are used, rather than removing them entirely. There might be ways you can remove them entirely (using create advantage rolls to improve odds instead, for example), but it might be easier to port in different systems to the setting instead.
However it shakes out, I hope you find a way to play a game that you enjoy in this fantastic universe!