Yay! New CI&A organization founded! I'll try to be as unbiased as I can.
Well, we need a formula. I've done several calculations based on other formulas and cards, as shown below.
Chance Bonus = Number of Chances +Abilities in question
Note :

= Other quanta, While

= different quantas combined
Wish is the example card. Unupped
Chances: 5, -1
Abilities in question : Holy Flash Player-Only (0), Weaker Precog (0.5

) ,Heal w/ purify counter ( 1

) , crusader (5

) , Miracle ( 15

)
Percent Modifiers result in the following values:
0
.1
0.15
.5
0.75
____
1.5 -> Rounds to 2.
Final Value: 1

Upped:
Chances 6, -1
Abilities in question: Holy Flash Player-Only (0), Weaker Precog (0.5

) ,Heal w/ purify counter ( 2

) , crusader (5

) , Miracle ( 12

) , Nymph (7

)
Percent Modifiers result in the following values:
0
.1
.4
.5
.35
.6
____
1.95 -> Rounds to 2
Final Value : 1

Card calculation
Spell
Unupped
Effect - Precalculated Chance Effect = +1
Bonuses : +2 as a spell.
Final Cost : 3

Upped
Effect - Precalculated Chance Effect = +1
Bonuses : +2 as a spell, but -1 as an upgrade. Final Bonus = +1
Final Cost : 2

I know the discussion may be over, but we should have something for reference the next time this happens.