Best of luck getting Mongoose to adapt any changes to the T/E system. When I last looked at this idea, it failed to impress me. My enthusiasm for analyzing further fixes (that in my opinion have no chance of being adapted by Mongoose) is seriously waning. If Mongoose adapts it, I'll spend some time analysing it in detail.
Like Michael Corleone in Godfather Part 3, every time I try to get out, they pull me back in...
I dug up the statistics I ran on your idea of reversing the order of results. Assuming that 2- is an exceptional success and that 5+ is a marginal success, here are the numbers for successful task rolls (not applying modifiers to timing or effect die):
-2 Modifier
1-2: 0%
3-4: 17%
5-6: 83%
-1 Modifier
1-2: 0%
3-4: 30%
5-6: 70%
0 Modifier
1-2: 6%
3-4: 33%
5-6: 60%
+1 Modifier
1-2: 14%
3-4: 34%
5-6: 52%
+2 Modifier
1-2: 19%
3-4: 34%
5-6: 46%
So, the better you are, the higher the chance of getting an exceptional success (and the lower the chance of a marginal success).
Here's how it behaves with failed rolls:
-2 Modifier
1-2: 40%
3-4: 36%
5-6: 23%
-1 Modifier
1-2: 46%
3-4: 34%
5-6: 19%
0 Modifier
1-2: 52%
3-4: 33%
5-6: 14%
+1 Modifier
1-2: 60%
3-4: 33%
5-6: 6%
+2 Modifier
1-2: 70%
3-4: 30%
5-6: 0%
So, the better you are, the higher the chance of getting a maginal failure (and the lower the chance of an abject failure).
Advantages
1. Overall, the system behaves far better than the current one, statistically.
2. Dispenses with the need to apply modifiers to the effect roll (and to the timing roll, which is currently *not* being done).
3. Somewhat less fussy, since you don't have to fiddle with applying modifiers directly to effect and timing die.
Disadvantages
1. Does not directly work with combat system, which is where the timing/effect silliness is worst. As you may have suggested, you could
subtract the effect roll from damage, which is somehwat clumsy but would work without having to alter the system. Base damage would have to be adjusted accordingly.
2. Excellent successes happen far more often than marginal successes. Marginal successes happen far more often than abject failures.
3. The system is extremely unintuitive. Now, high rolls are good, but really high rolls are bad. Since so much of the attraction of the T/E system seems based on the players' emotional response, I don't think that your system will have much traction. Personally, I like game systems to be designed so that either "high is good" or "low is good"; I've never cared for this type of blended system.
Conclusion
In my opinion, this system goes a long way towards solving the most glaring statistical problems with the T/E mechanic. But it remains fussy and is now unintuitive to boot. At the end of the day, I think that there are far easier and more intuitive ways to produce the same information. Nor do I think that the designer is likely to make what he'll see as a fundamental change to his precious system. So good luck on that; maybe I'll be wrong.