I know what you mean. For me it's not so much the train station, but the entire area. I guess FrL with Splash is better than without, but I can't truly get used to it. The area feels packed, crowded, claustrophobic. Without clear traffic patterns so everybody is in each other's way.
The old old train station also felt more natural, more frontier, than the modern large elevated one. The entire area felt more frontier than it does now. The empty lands leading up to a desolate, deserted Thunder Mountain felt more natural than the current set-up, from the wooden walkways in the river to the cartoons and the wet, southern swamp.