The core of this idea is that there are several (3-5) games of different types that share the same persistent world. Each game shows the world at a different level, but can still effect the levels above (and more dramatically) below it. I think the best way to really describe this is to outline the psuedo-hypothetical suite I used when first thinking of this.

Level 0: Universe: Colonies
A 4x space game where players are in control of a colony ship sent from far-away earth. In this new sector of space they must guide their people to becoming a major space power, while dealing with other players trying to do the same thing. Expansion, research, and military conquest are the major focuses, with a minor focus on economics and trade.

Level 1: Universe: Battlefleet
A space RTS (with homeworld-esque interface) where players control a fleet in the colonies. They can be hired as mercenaries by Level 0 players and fight in the wars, or be a simple merchant carrying goods across the stars. Either way the player can have a significant hand in how the universe unfolds by changing the course of battles, or ensuring that a fleet has proper logistical support.

Level 2: Universe: Commander
A ground RTS where players control armies fighting in planetary invasions started in Level 0. These players will be the deciding factor in wither or not a planetary conquest is successful. They can also call in on Level 1 players for orbital bombardments or additional transports of troops.
(I have also been thinking that this may belong as part of Level 0)

Level 3: Universe: Battlefront
An FPS where players are individual soldiers fighting on the front lines. Gameplay would be similar to the battlefield games, with the major exception that the maps are all procedurally generated based on colony
design by Level 0 players. Even at this level players can still help or hinder the war effort with effects ranging all the way up to Level 0. Teamwork would be most important at this level.


Of course this system has downsides. The Level 0 game will be the weakest of the suite; it's timescale will have to be widened to accommodate for the lower levels. The Level 2 and 3 games will be dependent on an invasion being started at Level 0, but I think I can get around this with training missions, robot rebellions, gray goo epidemics, and other "fun" happening occasionally on peaceful worlds that require a military response.

The reason I call this psuedo-hypothetical is because I'm already working on Universe: Colonies, but I don't intend to do anything on the lower levels until I have Level 0 complete and a team to help. Levels 1-3 aren't set in stone of course, those are just ideas.

Let me know what you think, thanks.

EDIT:
I forgot the major "selling point". Since each level is a distinct game the suite could attract a diverse set of players; each one playing the type of game they like.

Co-op gameplay at it's finest! I really like the concept of different players taking on different roles, with some kind of chain of command in place. I finished playing Valkyria Chronicles recently, and that kind of reflects a similar principle in a single game, albeit on a much smaller scale. Where you have meta-control over your squads strategy, deployment, EXP distribution etc, but also micro-manage each unit from a TPS perspective. It's a system I really enjoy, and the thought of expanding it for an in-depth multiplayer experience is something I can really see working.

One of the main challenges when designing such a thing that I can see would be dealing with the player's desire to be in control. In a typical FPS like Call of Duty, it's not a big deal to follow seemingly suicidal orders from an NPC commander because it is a single player experience, and you know the game is designed around you. So somebody else's decision screwing up your game isn't a big worry. With this system though, the people playing the foot soldier game are likely to become endlessly frustrated by the player on the next level up who tells them to 'Destroy this heavily fortified machine-gun-robot factory with your squad of 3 riflemen". The more levels you go down, the less influence you have on the success/failure in regards to the ultimate goal of the game.

CCP Games is doing this with Eve: Online (a space trading PC game) and DUST 541 (first-person shooter). From what I understand, EVE players will be able to hire DUST 541 players to do their dirty work. Or something like that. Here's a video teaser.

Cool.
Personally, I think it's the next step in video game evolution. I am a bit bias though, as I've been working on a similar idea myself. Good luck with your idea, ...it's a ton of work.

Have a look at "Global Agenda". This is a FPS MMO where players can play as individual troops that fight over maps like in any other FPS, but it also has an Agency vs Agency mode where you create or join an agency and try to take over a larger map strategically, however, the locations that are fought over in the AvA are the maps that the PvP players fight on and how each team does feeds back into AvA.

I love this idea, and have always loved it. My favorite manifestation, on a non-MMO level, was Battlefield 2 and BF2142. IT was just the bottom two levels of your idea, the RTS and FPS, with an intermediate "squad leader" role that helped sync the commanders with their troops. It was just a per-match game, but it offered such diversity and enjoyment that I couldn't get enough, and I'm always upset that Bad Company doesn't offer that depth of play.

I think the problem you'll face is the same problem that EvE expects to face: Participation. If I'm playing at the galactic conquest level, I want to have a certain number of troops, and a way to recruit and amass them, and some control over what they're doing. If my army consists of guys who love to play Halo, it'll be like herding cats. My army will be ten million strong between 6 and 11pm EST, and then it'll fall off to the 10k or so basement dwelling unemployed losers or second-shifters or Australians who are on after that, and the demographics and playtime of my individual soldiers will fluctuate wildly over the course of the day and week. I played some EvE, and major battles were always planned the same way: "Okay, these guys are mostly Russians, so we're going to hit them when their guys are asleep. They'll counterattack around 5-9am our time, so we need volunteers to call in sick and man the chokepoints during that time. Also, our French contingent have some wacky holiday next week, so we'll get a two-day boost in manpower, but there's a wildfire in California that's shutting down internet access for most of our command structure in the PST zone."

It's a real pain in the neck to try to work that sort of thing in real time.