Oh, is she just a strictly better version of him too? I admit I haven't looked that closely at her.
Not directly. They're actually very similar and I just prefer Sakuya a lot more.
Realistically, Sakuya is kind of what you'd get when you marry Ra and Anubis together-- a 25x low multiplier that's easier than Ra's and 100x high maximum multiplier that's more forgiving than Anubis' since it gives you in-between multipliers if you don't hit the 10combo.
Sakuya's easier to hit her 25x with, but Ra's easier to hit 100x with. But at the same time, Ra is either 1x/4x/25x/100x while Sakuya can be anywhere in between 1x/4x/25x/36x/49x/64x/81x/100x. Lots of chances to do great damage. See what I'm saying?
ASaku benefits from having a lot of utility and a more flexible team structure-- she doesn't need specific types like Ra does for his max potential. Granted, you can do likewise with Ra, but it's difficult to use him to full effectiveness without having fast actives-- you won't be getting any more than 25x without them.
Meanwhile, Sakuya is much more of a damage spectrum rather than Ra's binary "YES BIG DAMAGE" or "NOT BIG DAMAGE". It's easier and less resource-dependent to get her base 25x, and it's not at all very difficult to start bumping up the damage to 36x and 49x at 6c and 7c if you're packing time extends. Hitting the 64/81/100x multipliers often require a little extra luck or planning, but they're not limited by having to use your actives to get there, which lets you be a bit more flexible overall.
Sakuya also comes with built in bind removal/bind heal awakenings, and while they may be a use of precious gravity, it's so much nicer to have than not have. It's already saved my ass so many times, and I love her for it. People complain that it's counterproductive for her to waste a gravity for bind removal, but I say it's extra utility that means I don't need to slot Ceres or BMeta in, leaving me an extra space for a different stronger or bulkier utility. She just covers more of the playing field overall that way.
Sakuya's also got the gravity, which can definitely compensate for her less guaranteed damage. You can also strategically use them to break resolve, too. Damage the boss a little with x25 and then use the actives to break them under their percentage point so you can go in for the kill without having to risk triggering their resolve attack with an "unlucky" 100x.
However, she's not without drawbacks compared to ARa-- ARa's got a lot more HP and that goes a long way-- and his active is great for punching down stubborn high def enemies that require large combos from Sakuya. The time extend from that is also golden. ARa's damage is much easier to be guaranteed of, too-- you either have the big multiplier or you don't, and how and when that happens is up to you. Sakuya can hit it more consistently with luck and skill and timing, and can get in-between multipliers that Ra can't, but you can never be 100% certain of your odds of getting the multiplier you're aiming for, since perfect 10 combo boards are not the most common things ever. But still, reaching 64x-81x multiplier is also very respectable damage as well.
Ultimately it's a preference thing since they both can do roughly the same thing, but have different support needs. Sakuya needs support in the HP/damage reduction department because chances are your team will be pretty squishy, especially if you're loaded down with Kalis as healers. Thankfully, you can use Izanami or Susano or Indra or a Golem, etc and be fairly well covered there. She also greatly benefits from time extends/extend actives. I use ATsukuyomi for that. But the result is a team that's overall bindproof and skillbindproof with very flexible playing styles and fairly good RCV to keep the health up.
Ra is a more solid structure and doesn't have the same flexibility, and needs bind remover support (the ideal being Isis, of course) as well as someone with fast and disposable actives (also Isis), but hitting his maximum multiplier takes a lot less luck, time extends (5 combo vs 10 combo, no contest), and is a lot less prone to error for that reason.
That said, they're both good subs for each other, too. Sakuya brings great utility to Ra, and Ra brings bulk and time extend, as well as a nice pushbutton kill for stupid stubborn high def enemies.
They're both great, but my preference strongly sits with Sakuya for her flexibility and better sub pool. I think the quintessential "Ideal" Ra team is better overall though if you have all the pieces, since it takes way less effort to hit those big numbers because having 3 Kalis and an Isis means you're pretty much covered on all counts.