My understanding is that this narrowly defined verdict merely sets up the next round of litigation. We're still years away from any sort of fundamental conclusion.
This means Amtrak wins. Any win by the freights from now on (well, for a while, until the people on the courts and STB changes) is meaningless. The reasons for this are fairly subtle. In order to win, the freights have to strip Amtrak, the FRA, and the STB of regulatory authority -- a very heavy lift. With the direction this ruling is going, they won't be able to. Even if the freights get the "standards and metrics" invalidated on some other grounds, the Supreme Court has recognized explicitly that the freight railroads can be regulated to force them to provide quality passenger service *through* Amtrak -- whether they want to or not. (And that isn't dicta.) Alito even described contracts with Amtrak as a way of meeting their common carrier obligation, implying that he considers that if they didn't fulfill their contracts with Amtrak, they could be forced back into providing passenger service themselves!
Accordingly, the clause allowing the STB to investigate and decide on its own behalf whether to fine the freight railroads is on solid ground now. With a relatively friendly STB, that's a win for Amtrak service.
Will the Class I freight railroads continue to *waste stockholder money* on *frivolous lawsuits*? Very probably. I wonder if I could sue them for dissipation of corporate funds, since that's what they're doing. (It's been very hard to win such cases for the last 100 years, unfortunately.)
There's a subtle point at the end of Kennedy's ruling when he returns the case to the district court for resolution of other claims by the freights, and that's the "(if properly raised)" clause. Several of the claims were not properly raised. Expect another loss at the district court. It's possible that DC Court of Appeals will continue making up bogus arguments, but if so then the case will go back to the Supreme Court for a second smackdown. It's apparent only Alito and Thomas care about the goofy structure of Amtrak.