That could work as well. I'd have to see. Getting any sneak attack in GT is a bit of a pain, as you have to be at least a 3rd level Smart hero and most people going "rogue" will want Fast as well, meaning you often won't see any SA damage until 4th-6th level. That means Sneak Attack is best saved for "Assasins" and other higher-CR threats and PCs because by the time you get that, you've got quite a few other abilities and feats under your belt.
What I mean is, you're not getting alot of damage on even flat-footed foes until middle-levels. I seldom see games progress past 8th level before our plot arcs have rounded out and we're spiraling down the game. If you have Sneak Attack and no FDH, you'll start actually provoking MDT saves once in a while.
What I've found is that MDT comes up 9 times in 10 on Critical Hits. Most people in a MDT game won't leave Con at 10. Your average con is 12 or better.
Now, for me, the problem comes is that in all of my Modern/GT games, the focus of combat has been, naturally, on ranged weapons and firearms. They have pretty fixed damage outputs, unlike melee weapons, and REALLY the average damage is 5-9 points per hit. This doesn't threaten most people, or even mooks. So I get to the point where even when a hit threatens, it's been so long since the MDT rules come up, even -I- forget that it's a threat and a save should be rolled. We just wince and keep on trucking.
A good number of crits threaten anyway, and, as I said, most threats I've found are on crits. By making a house rule that all crits threaten, the MDT rule comes up often enough that we remember to use it. It adds a little to smaller, lighter weapons, which I like ... in D&D if a skinny guy comes at you with a dagger, after 3rd level you're liable to laugh at him. This way when I have a pack of evil assasins come bleeding out of the woodwork with their cruel curved knives the PCs get freaked.
But it's very much a style thing. If I were playing, say, Conan the Destroyer and wanted the focus to be on big muscley guys with broadswords and no shirts, I'd play down the flatfooted bonuses to remove some edge from ranged weapons and fast fellows.
--fje