Unfortunately the only Steam alternatives that have some amount of IPv6 support are Humble Bundle and Green Man Gaming. Though you may as well not count Humble Bundle as accessing their website over IPv6 results in it being completely broken [1].
I would like to see Valve get with the times on their v6 support though.
In the case of Humble Bundle breaking, it seems simply because some of their CDN subdomains are IPv4-only. Since the site loads various resources from those IPv4-only endpoints, it causes everything to just break when accessing over IPv6. In a way I'd argue it's still better than your browser displaying "no valid IP address for this domain" – usually you can at least find an e-mail address at the bottom of the page to alert them to the problem.
Just checked this in Firefox and it loads completely fine via IPv6 (and I verified using the devtools that it is using IPv6).
But mostly I don't want my games spread across a dozen different storefronts. Keeping them all in once place is more convenient. I would probably be more open to the Windows Store if I owned an XBox and there was some kind of integration, but I don't.