First let me say that, I came from XBMC and love the switch I made to PLEX.
One thing I do miss though is that while specials were grouped up in their own special category like they are in plex, they would also show up in the corresponding season based on air date. Take Doctor Who for example. Every year Christmas special, while it is a special it is part of a season and part of the story.
What would be a nice feature ( and maybe i just don’t know how to set it up) is that when browsing a show, to be able to list all episodes in a list, regardless of season. (so blow away the folders and show everything in one list) and then be able to sort that list based on released date, etc. that way I know where specials fit into the shows without having to check the internet to make sure I’m watching them in the correct order.