Man, that sounds frustrating! I wish I had the right thing to say to help you.
I also had a PC with "Stop right there!" who could stop anyone from Cheesing It, so I would let that happen, but sometimes I believe it's OK to use GM fiat to allow a character to escape if the circumstances reasonably dictate it. Like if they set off a huge bomb or cast a spell which opens up an enormous fissure in the Earth or have a plane come down and skyhook them out of there. As a player, I'd grant the GM that option once in a while without complaining that it ruined my schtick.
You mentioned an encounter which featured "over-powered uber-bosses" but nobody could hit the Ninja with an Attack Value of 14. Were the uber-bosses the ones with Attack AVs of 14? Because that's not really uber-boss level. Uber-boss is more like Attack AV of 17 to 19.
When I first started, I also found that most of my fights lasted only a single sequence. In most cases I was OK with this, because it still felt like the heroes were challenged. Over time I learned to fine-tune the encounters and add more mooks.
Are you playing remotely or are the players in the same room as you? Because if one of the heroes succeeds 8 Up Checks in a row, that's a little suspicious. At that point, however, they have at least 8 Marks of Death, don't they? After the fight they should pretty much collapse into little hero bits.
How dynamically are you and your players describing the action? I had prepared a silat-fighting knife-wielding guy based on Cecep Arif Rahman from The Raid 2. The Old Master leaped up to where he was and started Spinning Windmill Kick-ing him. This was during beta, so the Spinning Windmill Kick had no limits and he kicked the baddie successfully something like 6 times, taking him out in a single turn. The bad guy didn't even get to attack!
But it was such an epic moment that our players still talk about it, and I didn't feel like it was bad, I felt like it was a great moment for that player.
I think the "standard enemy encounter" is just a suggestion and you need to find your own balance for your party. (See this topic for some more discussion on this: https://forum.atlas-games.com/t/fengshui-gaming-day-questions/10685/1 )
If you've got a Sword Master or a Killer, they're going to mow through your mooks. Even before my heroes started getting advancements, I would throw 20 or 30 mooks at them in a single encounter.
I'd save the Boss or main Featured Foe until the second sequence. The mooks prevent the heroes from reaching the boss and the heroes must face them. Personally I prefer just adding more mooks versus trying to mess with mook attack values. They're easy to add and subtract from a fight.
I love talking about FS2 so I'm racking my brain trying to find ways to help you. I hope some of this is some help at least!