Cloud and Red share potential roles as all-rounders, with Cloud leaning more towards defenses and Red leaning towards speed. Having their Innate overlap isn't an issue because we want 1-2 characters to excel at any given role (all-rounder, offense, defense, speed utility), especially since Sega Chief lets you choose your lead character in Disc 2/3. It also helps that the .exe now alters Limit effects, so lower level limits are more valuable throughout the game.
Depending on whether you are playing on Arrange and whether you have Tifa in your party, reaching max stacks during boss battles will be unavoidable no matter how defensive you play. The battles where Cloud wouldn't stack much will be quick battles, in which case Red will also not get many stacks. This isn't counting post game where it's possible to end super bosses without taking much damage (thus not getting any limits) and have 255 for one or two stats.
Though you are correct, avoiding overlapping as much as possible is good i think. And the change i suggested makes Cloud innate go from "it will happen when it happens" to " I want the huge stat boost fast, thus i can afford to go all out-aggression". In my opinion it adds a bit more decision making on how you approach it.
Another example of this is comparing Vincents and Tifas innate. Vincents passive heal is based on current mana, thus you can alter how you approach it, more phys dps/tank, or waste mana as a mage and lose some of the healing. While Tifas just happens when you get bursted down.
Now this wouldnt be a problem since we already have "passive" and "active" innates (what i call the scenario above) in other chars. But since Red is already the "Passive" one of the all-rounders, Cloud could potentially be the "active" one making it more engaging (in my opinion of course).
I could change this myself with WallMarket but i suck with scripts xD
EDIT: Just came up with an idea that would retain the all-around feature but add a bit more flavour to this innate.
5 stacks
Each stack gives 4 STR/MAG (= 20 in both at max)
When reaching 5 stack Cloud gets 15 VIT/SPR.
This allows Cloud to choose a aggressive style and be rewarded with defensive stats for getting alot of limits off. While also being able to go at it more slowly and getting boost along the way, "cementing" the defensive style when reaching max stacks
Ofc the numbers can be tweaked to lets say 15 total overall ( STR/MAG/VIT/SPR)