I think any changes to ability scores bonuses will have to go hand-in-hand with how important the opposed roll becomes in the game. In fact, we don't know if the opposed roll will be like a classic opposed roll, or whether it will simply give a small modifier to the saving throw (although I doubt this will be the case).
In the classic case both roll a d20 and add their bonuses, and the larger result wins. If D is a random variable = random d20 roll and d is the defender's bonus, and A is a random variable = random d20 roll and a is the attacker's bonus, the probability of an attack succeeding (assuming the defender wins ties) is:
A + a > D + d, equivalent to A - D + (a-d) > 0.
A - D is distributed as d20 - d20 (independent rolls), which has a probability distribution that runs from -19 to 19, and is shaped like a triangle with a peak at 0 (a 5% probability). This is a much wider range than a single d20 roll, but it is also more forgiving to large differences in the bonuses because the "average" outcome is more likely than the outside ones. If we assume the 3.5/4e method of ability score bonuses, and assume ability scores will generally range from 2 to 20, the largest usual a-d will be 5 - (-4) = 9. Even in this case, the attack succeeds only 83.5% of the time, and slightly lower than that if a natural 20 on a save always succeeds. In 4e the equivalent (ignoring class adjustments and so on), would be a +5 attack vs. defense 6. In other words, the attack succeeds 95% of the time. In 3e even a 1st level spell would have a DC of at least 16, so a character that starts with no other modifiers to this particular save would need to roll a 20. And in both 3e and 4e the disparity will tend to grow wider over time.
In a more typical case, say an attacker with 18 vs. a defender with 10, the probability of the attack succeeding is d20-d20+4 > 0, which succeeds 66% of the time (again ignoring natural 20s saving). In the case of 4e that would be like a +4 bonus vs defense 10, which has a 75% chance of success. The point is, for any method of calculating bonuses from ability scores, opposed rolls are more tolerant of large differences in ability scores than rolls against static numbers.
Now consider the relative benefit of higher ability scores in 5e if using opposed checks. When a-d is close to 0, each additional +1 is almost the same as in the static case. For example, when a-d is 0 the attack has a 47.5% chance of success, but if it is 1 it has a 52.5% chance of success. If a-d is 2, however, it becomes 57.25%. If the best offenses and the best defenses basically rise together, that means (assuming 3.5/4e ability score bonuses) going from ability 16 to ability 20 would give about a 10% improvement when attacking a target's best defense much like in 3.5 and 4e. However, if one targets an opponent's lowest defense (the more usual strategy), the change is smaller. Suppose two wizards (16 and 20 Int) try to charm the classic dumb fighter (8 Wis/Cha). Then a-d is 4 and 6, respectively, and the first wizard has a 66% chance, and the second a 73.5% chance, for a 7.5% improvement. Whether or not that is still too great a difference I'll leave to you.
The opposed roll has an additional element, in that if the attacker rolls sufficiently high the defender will often need to roll a 20 to save. This is conditional probability, however, so a specialized attacker can't count on it when choosing what to do. One of the more exciting elements of the game is needing to roll the clutch 20, and this will make those moments more frequent without screwing everyone constantly. There is also tension in the game by making the players wonder *if* they'll need to roll a clutch 20 against this next fireball. Even a person with a very good defense will face that on occasions.
I suppose the opposed roll is a little weird in that it will feel more swingy (there will be some pretty wild outliers and they will occur unpredictably) even though it actually tends more to the mean than a single d20 roll using the same ability scores and system of bonuses. For example, fifty percent of all outcomes for a single d20 are in the 6-15 range, while (about) 50% of all outcomes for d20-d20 are in the -5 to +5 range. They have the same absolute size, but different sizes relative to the number of possible outcomes. This is why looking at opposed checks and thinking the bonuses should be twice as large to account for twice as many possible outcomes is a bad idea.
Finally, using opposed rolls probably adds a single extra roll to what we'd expect in either 3e or 4e (that is, the attacker does not roll one for every target). At least in my experience the number of d20 rolls was not the primary cause of slowdowns. If the rest of the game is designed to keep things moving we might not notice a single extra roll most turns.
In summary, I don't think we'll necessarily need to change the way ability score bonuses are calculated, because opposed checks using the 3.5/4e method still tones down some of the strongest disparities due to static checks found in 3.5/4e, and introduces modest diminishing returns for increasing ability scores. Whether that will be enough to discourage the worst min/maxing and prevent the worst relative disparities between characters will depend a great deal on other factors. In either case I think understanding the math of the opposed check is important.