I wouldn't say that's inherently inevitable, although I do understand and agree with your concern. It's something they need to keep in mind going forward for sure.
The main deciding factor is going to be how far the general population ends up spreading out, and how many/what kind of reasons you'd have for traveling great distances. If we see clusters of stations form "neighborhoods" then it shouldn't be an issue. If your destination is a mere fifteen minute flight away then traveling by capital is obviously going to be needless overkill regardless of charge time. It only really starts to unbalance there's some unavoidable reason for you to constantly be going from one far away place to another, and not doing so puts you at a clear disadvantage.
It's kind of hard to predict in advance how that sort of thing will play out, so I imagine some trial and error is unavoidable before they're properly balanced. That should be a given with a game of this size and scope.
Will they make manual freighters obsolete? Sort of, probably? Personally I think the ability to transport large amounts of resources over great distances is a suitable reward for building the thing in the first place. That's probably going to be beneficial in the long run, as it will hopefully make spreading out a lot less painful for people and encourage a more inter-connected economy. If it makes you feel any better you can think of it in terms of capitals being cargo ships and manually piloted freighters as trailer trucks: The cargo ship being able to transport more stuff farther doesn't make your job as a truck driver obsolete. They're similar but still distinct niches.
Will they invalidate stations? Doubtful. There's plenty of things that can be made exclusive to stations if everyone starts minmaxing themselves into space Mongols. Stations are currently just glorified storage units so I expect people will probably live out of capitals for a period once they're added, but that's less to do with capitals being superior and more to do with stations specifically just being bad right now.
The main deciding factor is going to be how far the general population ends up spreading out, and how many/what kind of reasons you'd have for traveling great distances. If we see clusters of stations form "neighborhoods" then it shouldn't be an issue. If your destination is a mere fifteen minute flight away then traveling by capital is obviously going to be needless overkill regardless of charge time. It only really starts to unbalance there's some unavoidable reason for you to constantly be going from one far away place to another, and not doing so puts you at a clear disadvantage.
It's kind of hard to predict in advance how that sort of thing will play out, so I imagine some trial and error is unavoidable before they're properly balanced. That should be a given with a game of this size and scope.
Will they make manual freighters obsolete? Sort of, probably? Personally I think the ability to transport large amounts of resources over great distances is a suitable reward for building the thing in the first place. That's probably going to be beneficial in the long run, as it will hopefully make spreading out a lot less painful for people and encourage a more inter-connected economy. If it makes you feel any better you can think of it in terms of capitals being cargo ships and manually piloted freighters as trailer trucks: The cargo ship being able to transport more stuff farther doesn't make your job as a truck driver obsolete. They're similar but still distinct niches.
Will they invalidate stations? Doubtful. There's plenty of things that can be made exclusive to stations if everyone starts minmaxing themselves into space Mongols. Stations are currently just glorified storage units so I expect people will probably live out of capitals for a period once they're added, but that's less to do with capitals being superior and more to do with stations specifically just being bad right now.