3 way, red is (usually) the traveler, and yes you're basically screwed with a traditional setup.
Nobody runs multiple loops for that, just supply to the box nearest to panel usually, then run the 3 conductor to the second switch, then two conductor to the load.
Options are you could bypass the first switch with line power by passing it up to the second switch and blank it out, or vice versa by just tying the black off to the load and removing the traveler. You might be able to use the secondary switch to control a light in the first box using the traveler but that is about it.
However you could get something like a z-wave smart switch and use it to trigger a routine on another light, but you'd need two smart switches and a controller for that.
https://en.wikipedia.org/wiki/Multiway_switching
Multiway switching is a lot less scary than it seems, its really just a conditional toggle at that point, the traveler carries the line in the "off" position and then the second switch gets the decision, etc.