At what point is Mewtwo's Disable most effective?

999% will stun the opponent for the longest. No other factor than damage influences the stun duration, except for control inputs from the opponent which will reduce the duration.

Unfortunately, the neither the Smash Wiki pages for Mewtwo nor stun are very useful for determining the stun duration of Disable.
However, apparently Mew2King (one of the best Smash Bros. players ever) discovered some of this type of information in Super Smash Bros. Melee. Quoting from that compendium of information (note that 60 frames is equal to one second):

Mewtwo Disable Escape Speed Formula – the formula for how long it takes the victim to escape Disable can be found by this formula, and the variables are the following: “t” is the time(in frames) a foe will be disabled, “b” is the amount of times the victim presses the buttons on the control stick for escaping quicker(1 rotation of the control stick = 4 button presses, and every button press is 6 frames less you’ll be trapped by the move), and “d” is the damage of the victim Disabled.

[...]

The formula is…

t = 0.6d + 95 – 6b

This is followed by a list of values for the stun duration, which goes up to 400% and 336 frames of stun. Mew2King also states a value for 999%:

999% – 696??? (11.6 sec)

Therefore the duration of the stun is linearly proportional to the opponent's percentage, at least in Melee it was.

The Smash Wiki change list for Mewtwo states that the stun duration has increased in Smash Bros. 4:

Disable's stun duration has increased and its lag has decreased, making it much more reliable as a set-up.

It is not stated the equation has been changed from linear, or that it now caps at a certain percentage. Therefore it is probably safe to infer that 999% will still result in the longest stun. I did some testing to confirm this, with the following results (without any control input from the stunned opponent):

100% - 3.71s
200% - 6.04s
300% - 8.28s
400% - 10.81s
500% - 13.07s
600% - 15.38s
700% - 17.68s
800% - 20.03s
900% - 22.35s
999% - 24.73s

Clearly it is still a linear relationship, and the stun duration appears to be roughly double that of Melee.

This is pretty easily tested in training mode: Disable stuns opponents for longer when they have higher damage. Of course, like most other status effects, they can escape faster by mashing buttons. The effect of weight is negligible.