Balance issues should honestly not arise as long as they gate the amount of powerfull abilities in one commander by some kind of points. For example ou would get 500 at max for your commander and is-2 call in would cost 350 so you cant stack a b4 in the same commander...
Well, there are already commanders with 3-5 good abilities and then there are those with 0-2.
If is2 would take 350 out of 500 as you suggested, then double t34-85 would be less than 150, because we already have that combo with three other abilities as well (armored assault). Basicly I´m saying it would have to be a little more complicated than that.