I think the answer to that question is similar to the answer to the question "what was the end game for the entire game?" The answer is: the devs didn't have an "end" to their end game plans.
"End game" as an MMO term is a bit of a misnomer in that its not about an "end." The "end" in endgame refers to the point where conventional level-gating (cf: level cap) ends and content switches from being about getting through the next content gate and starts being about more open ended (if often grindy) development.
What I think was interesting about CoH's "end game" was that it wasn't, in spite of complaints to the contrary, focused purely on raiding. The initial content was large scale raids, but that was because we didn't have any yet and this was when they were going to be introduced. But the revamp of Dark Astoria suggested that the incarnate system was going to be a more seamless expansion of the standard content, with zone content, mission content, and task force content to complement the raid content.
This ventures into a subject I spent a lot of time kicking around on the old forums: what constituted the "core" game and what constituted the "optional" game. You could argue that the Incarnate system was evolving into Yet Another non-core gameplay mode. The standard game was the conventional content-based (usually) leveling from 1 to 50, with the associated power and enhancement progression. The incarnate system as a whole was developing from a raid niche to a more full-fledged game experience with a range of content driven by the core incarnate power system and the raids as a strong core component of progression.
Of course, many people who disliked raiding and disliked the incarnate progressional power system felt that time spent developing it was time diverted from the rest of the game, and player time spent on it diverted players from contributing to the rest of the game. Both true statements, but also entirely in keeping with the philosophy I subscribed to and generally ascribed to the devs as "something for everyone, not everything for someone." Part of acknowledging the fact that CoH allowed for diverse playstyles is that it often encouraged and spent valuable dev time on ones you might dislike yourself personally. I think eventually the great irony of the Incarnate system is that the very players that were complaining about the fact that it was about nothing but raiding would eventually be complaining about the fact that there was all this other stuff happening in it they couldn't experience because they didn't want to participate in the incarnate system.
Optional isn't synonymous with undesirable.
This.
The one thing I kind of HOPED was going to happen was that the Devs would take their original approach to "end game content" which, in my opinion, were the HEAT and VEAT achetypes, and combine that with the Incarnate progression system with the Omega slot. Really, to begin building an "end game" that was neither purely "grindy" nor simpy rolling a new kind of alt, they needed to try and work in the entire game. A "hybrid" of the three approaches of "end game grind, new content, and rerunning earlier game content, if you will.
What do I mean?
Well, just as an example...
Imagine that the Incarnate/Well storyline, the Oroborous/Mender Silos storyline, the storyline hinted at in the side switching arcs of your undoing the Universe, and the storylines of the 1-50 content all "intersected" with the Omega slot.
The original approach with VEATS had you unlocking unique archetypes and then rolling characters that were "leveling" alongside regular 1-50 characters, but also had their own story lines and contacts supplementing that experience. Imagine that the culmination of the Incarnate story line put your character in the position of being forced into a dilema: the only way to "save the universe" from Battalion (who were consumers of the Wells) was to consume the wells, and all of their power yourself, in essence becoming the "uber being" that your future version warned you about in the side switching story lines. Essentially, you not only go the route of Emporer Cole, but you go one step further, actually tapping all of the power of ALL the Wells the Battalion had consumed. Mender Silos warns you that in the future he comes from, this was a plan he encouraged you to take, and doing so, ultimately lead you to becoming as much a threat to the freedom of mankind as the Battalion or Rularru, since you're only a flawed human not meant for omnipotence. Since you'd have absorbed all of the power of the Wells, and thus the potential energy of every living being in the universe, there were no one heroes left to try and stop you.
What's worse, he doesn't go in to detail but states that your actions will awaken the interest of "those even higher than Battalion, even the Wells", and be the undoing of the entire universe. He came back in time to try and prevent this mistake from happening again. He gives you a third option, a NEW Nemesis plot, however, which would require the Dream Doctor's help: You consume the wells, defeat the Battalion, then "give up" your omnipotence by destroying your own sentience, willingly allowing the Dream Doctor to imprison your mind in a separate dimension. You become a new Well, restoring power to heroes around the universe, but also a better "Well." Unlike previous wells, you will give up all self will, self awareness, and sense of self preservation. Your ID is separated from your body, trapped forever away from the new Well and the very universe you saved.
This story line unlocks the Omega slot, where your character, still a level 50, has a whole new set of missions unlocked throughout the regular 1-50 game. Of course, Lord Nemesis isn't completely honest, and after you've killed yourself, you are awoken by Mender Lazarus who tells you that your sacrifice worked, but had some unforseen consequences. Your restoration of the wells was not perfect, and the timeline -and the power of the well- is in a state of flux. The well, absent any sense of sentience, is unable to "choose its guardians", and its power is now more easily manipulated and tapped in to. Some entities are using this as a chance to steal the power of the Well, even altering key moments in history to gather more for themselves from those who otherwise would tap in to it. Mender Lazarus has restored your sentience to an earlier version of yourself, (weaker than your omnipotent version but still level 50, still in possession of many of your incarnate powers, etc) to try and correct things. To do this you basically have to reexperince key events of your life, guiding events to make sure that they occur correctly, stopping new threats trying to gather your power for their own purposes, etc. These new experiences come from contacts you had before, as well as new contacts like Mender Lazarus.
If the technology could be worked out, do something along the lines of what you have with the Nictus and Void Stalkers and HEATS, where when an Incarnate is on the team and is team leader, the villains in the mission spawn as their incarnate level versions, but the mission itself remains the same. So running the Maria Jenkins missions would run the same, but have Incarnate level versions of the baddies if it's an Incarnate's mission. Also have contacts give additional missions that occur "alongside" the normal missions from the 1-50 content, where you're working to set things right once and for all. Imagine running the Hollows missions again, only facing Incarnate level Hellions and trolls, using the power of the well to fight you and your team. Or you're given an extra mission from a contact in Faultline where the 5th Column are trying to kill your younger self as he completes the 5th column Task Force so that you never become a well in the future. Imagine a single mission given out by Mender Lazarus where you're level 50 incarnate self is fighting a Council attempt to alter the moment when your previous self and 7 others defeated Romulus in ancient Cimerora, and their attempts are resulting in "hiccups" in time. It would be a fun single mission fighting Incarnate level Council, tie in to the regular 1-50 games missions and stories, and even give an explanation for the crazy lag during an ITF. :-D
This way the "end game" is simply "the game" in all its facets. It includes all of the end game raids, but also reliving the older content in a new way that is still a challenge and makes "sense" from a narrative perspective, and yet doesn't negate your level 50 status or incarnate achievements. It encourages those "opting in" to incarnate content to still team with those who either haven't yet been able to or have chosen "not to."
The story line above is just a poor example of how they could do it, but to me, this sort of hybrid approach of avoiding simply raising the cap, while also avoiding just grinding "raids", and encouraging incarnates to still play with 1-50s AS part of the
end game content that still feels "new" would be a perfect balance.
And honestly, with a little creativity, someone could write a story line where the three major story lines of the game explain it perfectly for something like this.
It would mean creating Incarnate level versions of all the villains in the game, just like they did the Tsoo, but really, how much harder is that than redoing entire zones and contacts, or adding altogether new ones?