Go with wired networking or be careful about your choice of WiFi hardware. Some wireless chipsets have poor Linux support, but there are usually lists of good ones and bad ones. When it comes to graphics, AMD GPUs Vega or newer work incredibly well on Linux. NVidia has a fairly substantial lead in GPU performance, but they have poor Linux support and appear to be actively working to make their hardware a bad deal. Most motherboards have no issues on Linux, but audio and networking can be pain points. CPU brand is not an issue with Linux, but since your choice of CPU and choice of motherboard are tied together, it is something you might have to think about. Perhaps pick a price, find AMD and Intel motherboards that support the features you want and have good Linux compatibility, and then figure out which brand gets you better performance at that price with your desired feature set.
Hardware that requires a proprietary windows app to control can be a problem - think RGB hardware and fancy gaming mice. There is some software to work with these sorts of things and you can get Logitech gaming mice working on Linux but it is somewhat harder than it should be. Stay away from Razer - their software is more troublesome than anyone else's.
Steam has absolutely incredible controller support. It is ludicrously good. If you want to play games on PC with a controller, hope they're Steam games or at least work well when launched through steam.
Use PCPartPicker when you're putting together your build. Their website is a wonderful tool for checking compatibility even though it's not perfect. If you ask someone for advice on your build, being able to give them a PCPartPicker link really speeds things up. If you're looking for a place to get advice on a build, /r/buildapc is generally decent.
If you're concerned about upgradeability or future-proofing, it's not a great time for that on the CPU front. AMD's AM5 socket just came out and probably has a good few years ahead of it, but the first-generation motherboards are awfully expensive and you should never buy first gen mobos anyways. It is also quite possible they will have poor support for Zen 5 CPUs. Intel's LGA 1200 socket is obsolete and current LGA 1700 motherboards probably won't support anything past the 13th generation (Raptor Lake). That said, a new mid or high-end CPU is likely to remain useful for many years since popular games are somewhat limited by the need to support 9th gen consoles. Similar is true for GPUs, but GPU prices are not great at the moment though they are better than they have been in the past few years.
If you have any other questions let me know.