Really? With the train station in Kyoto? Seriously? I've been there, both in the train station and in the surrounding area. It's big, but it's not exactly skyline wrecking unless you happen to live in an apartment which directly faces it. There are plenty of other buildings nearby which are close to the same height and once you get about two blocks away, you can't even see it from the street. If you don't believe me, here's a picture from above which shows the surrounding area. Plenty of other 8+ story buildings in the area. Here's a view from the top of the hotel in the train station. What skyline is it that they're destroying exactly?
Kyoto is a lovely city. It has myriad beautiful temples and gardens and the nearby country-side is lovely. People flock to it to see the cherry trees when they are in bloom. But none of these things are very tall. Most of the famous temples aren't even visible when you're half a block away from them, nevermind part of the skyline. It does not now have an impressive skyline and if it ever did, it must have been centuries ago, and although the train station big enough to be clearly visible for a couple of blocks around, it's not exactly a sky-scraper. Honestly, its width and shininess stand out as much as its height. So, if the person writing the article thinks that the Kyoto train station (which has far more non-shinkansen platforms than shinkansen platforms) is too big or too shiny, then fine, but saying that it wrecks the skyline is just dumb.