Yeah, it definitely messes with the odds a little bit, though I think the overall effect might be a good one. In particular, as you say, it encourages you to gamble a bit more, which makes it more likely that permanent stress accrues. Currently, if I have 4 stress, risking 1 more (permanent) stress to get 1 or 2 activations is rarely worth it unless it’s something like an RPG shot at a tank. If I had a chance of getting a “burst” of 5 or 6 points, then that’s a very legit gamble but I have to balance that out against starting the next phase with more permanent stress. It might make long-running games a bit more interesting because you have to pace yourself more.
I use the “alternative” method and find that you get a lot more activity, which I like. I thought that the “original” method, subtracting your stress from a D6 and Exhausting-out if you get a 0 or less, was too limiting.
That being said…I might revisit the original activation method now that the Move Out/Suppressing Fire rules are there, where you can spend 1 point to do something with 3 troopers.
Something else that I use as “standard” which is optional is the 3″ assault range in No Stars in Sight, for fighting in complexes. I use that for Assaults generally; forces the players to do more of the fun fire-and-maneuver that makes the game shine, and offsets, somewhat, the additional activations possible with the alternative activation rule.