I completely understand the concerns. What you're currently seeing in Alpha are bits and pieces of a system that is still coming together, untuned and often even inconsistent between classes, without additional context. And as a result, there's also a fair bit of misinformation floating around (for example, the cap on active champions/followers is 6, not 20). We haven't published a full explanation of the system, because we're still working out a few of the details - that's the nature of Alpha. And of course in the absence of information, seeing an interface that looks a lot like a reskinned version of what you're used to in Draenor garrisons (followers -> champions, garrison resources -> order resources, etc.), it's easy to assume that this is just a continuation of the old system.
I'd like to at least shed light on some of our goals and philosophies, and the core ways in which Class Order missions in Legion are going to be very different from garrison missions in Warlords. The mission system in Warlords was conceived as a core part of the garrison experience, and a self-contained progression that offered rewards that competed with other traditional content.
We approached Legion unsure whether there would even be any continuation of mission gameplay at all. We focused instead on the artifact and class order systems, creating traditional content to provide the experience of forming a band of the greatest champions of your class to combat the Legion, with an eye towards class identity and replayability. We want your journey through the Broken Isles to feel meaningfully different in at least a few key ways depending on whether you are a mage, a warrior, a demon hunter, etc.
Once we had the backbone of our order systems in place - a campaign quest arc wherein you recruit champions to aid your cause, and an order hall tech tree where you research upgrades - we saw what seemed like a good fit for a version of the old mission gameplay to provide another outlet for leading the champions you've gathered, and spending the order resources you've earned out in the world. But it is far more limited in scope, and designed to be a much smaller piece of Legion than missions were in Warlords - it's serving a larger system, rather than trying to stand alone as a system in and of itself.
There are fewer followers (champions), fewer and less frequent missions; but more importantly, the system is more closely tied to the game world itself. Order resources come from playing the game normally, and will come primarily from doing World Quests at max level. If you get a "raid mission," it won't give you a piece of raid loot directly; it will give you a quest to kill a specific boss in that zone, in exchange for a bonus piece of loot. In general, from the ground up, missions in Legion are not intended to be an alternate progression path, or a self-contained activity. We don't think of them as "content." But they are a useful additional outlet to complement core traditional content, such as dungeons, outdoor questing, and raids.
We'll have more details to share in the future, but hopefully this helps clarify some of our broader goals and provides some context to what you may be seeing in game.