'Should I R now to help finish, or do I need to save it for a kill?' in your suggested change simply becomes, 'R when low health.' It's not that there's constant strategic value to using it on high-health targets, it's just that the potential exists now as the skill is and it still does execution just fine. Caitlyn doesn't scale to missing HP (at all) because she gets range and speed. Jhin gets range, but not speed, so he's got the missing HP as a chunk of his damage goes AWOL to having to reload, static attack speed, the like. (in theory, anyway... bear with me there)
Cait's got plenty going for her as she is and if she receives changes it should probably be to some small things-- the way Runaan's behaves with her passive, her scaling, maybe mana costs and/or cooldowns. Adding missing health scaling feels like it would push her one way or the other a little too directly.
On another note for that, it would be lining her up with Jhin and Jinx who already have long-range execute ults. Variety is very healthy, especially with 123 champions; if tons of champions just end up with '% missing health damage' as ult mechanics, isn't this pushing the game in a direction everyone frags Riot for taking (IE homogenized champion design)? Cait's ult is just long-range single target. In exchange for being a lump sum of damage with no strings attached, it can be intercepted. It has its own workings and that seems to work just fine for her as most of her kit follows that train of thought (deadly, long range with plenty of room for interception).