The 4690k may not be the best/most modern anymore, but it was a favourite for gamers for a long time. That's probably what you've been reading, since the 4690k has been out for a comparatively long time so there would exist more recommendations for the 4690k than any Skylake processor scouring the web. Bear in mind that if you get a 6600k, you will have to get a motherboard with a x170 chipset and also DDR4 memory which would probably cost more altogether since it is relatively new technology. I'd say that the i5 4690k is still a solid performer and should give you what you need when it comes to gaming.
Yes, you will have to re-install Windows when you replace your motherboard, unless it is the same motherboard. Even if your PC runs without having to re-install, re-install anyway.
If you are going for the 4690k then get something with a Z97 chipset. If you are going for the 6600k then similarly get something with a Z170 chipset. Just searching for "Z97 motherboard" or "Z170 motherboard" will give you a lot of options, then it's just a matter of choosing one that's in your price range and that has decent reviews.