The following represents how I hope to structure and organize the "games in my backlog" to ensure desired functionality in the What Should I Play menu and, to an admitted lesser extent, my Mission List.

Backlog
As it stands, I strive to keep the "games in my backlog" current at the point of the series at which I've progressed, and no further; this is such that if I were to use the What Should I Play functionality, I would not be given a game later in the series than where I am - i.e. being told to play God of War Ragnarok when you haven't played God of War yet. It will also prevent Missions from being assigned for content I haven't reached, though I also have a Mission List I intend to keep up-to-date serving the same purpose. It's redundant bookkeeping, but I enjoy that sort of thing.

[EXCEPTIONS: For series like Fallout, Final Fantasy, or The Legend of Zelda, where each game is a relatively self-contained adventure, this rule is waived. In the above example of God of War, I may argue the PS4 reboot is a big enough departure that I would allow someone to assign me games from either Kratos' Greek or Norse Era. Reboots, in this sense, are treated as a new series entirely.]

Add-ons, Mission Packs, DLC

DLC is also delisted from the Backlog, working by the logic that if I were to play their game, I would also play the associated add-on content. This is also why I add episodic games via their Compilation - if I were assigned Sam & Max Save the World, I would play the whole thing.

[EXCEPTION: Standalone expansions, provided they are not directly tied to their base game's story, are considered different games. Far Cry 3: Blood Dragon can be played without playing Far Cry 3, but FEAR: Extraction Point cannot.]

Shared Titles on Multiple Platforms

My rule is to mark all similar copies as Finished across all appropriate platforms (which I own the game on), and not where the game is significantly different between releases. This is to cover handhelds and downports of games where they can prove to be exceptionally different experiences.

Furthermore, if a game has been Completionated, regardless of similarity, I will only mark it as such on the platform I attained 100% on. A live example of mine would be Spyro: Reignited Trilogy, which I've only 100%'d on Steam but also own on PS4, and some of my LEGO games.

TL;DR I am not playing Doom 3 on Steam, PS3, and GOG separately. You can't make me. I would 100% them separately though, if I were so inclined. Doom 3 accounts for 24 entries in my library, for cripes' sake.

"Endless" Games

Games which I consider to be "endless" will likely never be available on my Mission List. However, they will be kept Backlogged so the random game selection can select them, and I'll log completions of runs as would be expected. This is for things like virtual board games where you can finish individual playthroughs without really "beating" the game, and games that run as long as the player is willing to continue.

TL;DR I will not allow you to assign me Animal Crossing. If I'm playing Animal Crossing, it's because I chose to, you're not my DAD-

--

So, what do people think? I'm hoping to get to work reorganizing my library as such and getting my Mission List nice and ready to participate in the Mercenary Guild; it's still a work in progress at the moment.

I'm also open to questions or further suggestions on how might be better to structure things.

Sounds like a solid plan.

Like the completion status everyone does it differently, so no right or wrong.

I for example do it kinda differently. I have quiet the library at my disposal and can seldom decide what to play, even If I start a playthrough I jump games pretty fast, which in turn hinders my completion goals.

Now in my System every game starts in the backlog. Normally I play games which are either bounties or on my shortlist/Goal list, when they are finished I set the status to finished or completionated. Games which are only finished are added to my "Need to Completionate" list which is also my mission list for the guild. When the game appears again on my goal list or via guild mission I play them to the next stage of "completeness" (which differs from game to game. For example I played the story, but now I collect all collectibles or defeat all hidden enemies etc.). If the game in question is already completed, I play them on a different platform/alternate version or do a challenge run.

You know, a "Need to Completionate" list isn't a bad idea! I might need to look into one of my own, though my backlog is such that simply beating games is still pretty important.