I'd like to see native MP4 and MKV tagging as well.
Unfortunately, the biggest issue is performance. Adding tags (to a MKV file, for example) typically requires remuxing the entire video file, which means it could take 1-5 minutes on average hardware to write tags to a single large BluRay rip, for example. On slower hardware, it could take 10-15 minutes. Plus there are a variety of risks to data integrity (making sure things like various streams stay synced and whatnot). As frequently as MC updates tags here and there in normal usage, obviously these things couldn't be done "on the fly" as it does with MP3 and FLAC files. The performance required is an order-of-magnitude off of what would be required.
Another issue is that there is no well defined "ID3-like" standard that is widely agreed upon by the software industry for video. So, MC could store its own tags in some file types (it would take a bunch of work because MP4 and MKV, for example, use very different systems for storing tags), but these tags would not work well in any other applications except MC itself.
So, this would be of limited utility and would be difficult to implement well.
Perhaps some day, but for now, the sidecar files are a reasonable alternative. If they did implement it, I'd love to have the ability to manually "push" the tags into the files (via Right-Click > Library Tools > Update Properties from Library), but keeping it "always in sync" would probably require the sidecar files for the foreseeable future.
Unless Hendrik can really work some magic here, anyway.