I saw confirmed by Luke in another thread that the three levels of Traits are not cumulative. Got it.
Just to be clear, using a Trait doesn’t bump it down to the lower level, correct? E.g., if a player uses a Level 3 Trait, it just means that Trait is used up until recharged. It doesn’t mean that the Level 3 benefit is used up, and now it bumps down to Level 2, which can be used, and so forth. I figured not, but I wanted to be clear.
It does make me wonder if Level 2 is the most useful, though.
As far as I read it, that’s correct. You basically don’t have the lower level trait at all, just the improved version of it.
Same here. 
A call on is way more powerful. And you can spend checks to recharge it.
My players tend to disagree; they generally feel (and I agree with them) that a level 3 trait is less powerful than the level 2. Rerolling the traitors can be a help, but it’s overall less advantage than +1D on many rolls. (Especially, given my group, the level 3’s have been bold and rational… very useful traits.)
A level 3 is far more powerful than a level 1, tho.
Your players have taken the short term, immediate gratification path. However, +1D is nice, but NOTHING is more powerful than a call-on when you’ve failed a test, rolled no 6s and death is on the line.
Ah, I didn’t know a call-on could be used after the roll!
At what other time would you reroll?
… Well, the alternative being that it acted like Persona; ie, I always thought a call-on had to be decided on before the roll.
Persona is always after the roll. Fate is always before.
Reverse that. 
You spend Persona before the roll and Fate after the roll (if you get any sixes).
Duh. Morning, brain fuzzy.