What I hate about the endgame is you end up with all these soldiers you're telling yourself these little stories about, and all this cool shit to use, and you know its just leading up to picking 6 of them to do a boring scripted mission that's easy until the overly difficult final fight.
What I think would be cool is that in the later part of the game you and the aliens take turns essentially placing down assets into the extended final mission. So like, let's say past a certain midgame story mission, both Xcom and the Aliens realize its going to come down to a final assault of the aliens on humanity. So the aliens get preparation actions like "Mech battalion," or "WMD strike." And each of those sets up a bad outcome. "WMD strike" could permanently destroy a region, "faceless infiltration" or "mech battalion" would set up lategame missions, and things like "transport battalion" and "command center" could set up advantages for the aliens during the final missions. Xcom would get missions, not to counter these preparations, but merely know what they are. To counter the preparations, they would have to go to each region and permanently place down their own resources. They would lose access to these resources for the rest of the standard game, but then for the lategame the placed down resources would be all they have. So, for example, to counter the WMD strike they could send 400 resources and an engineer to a region to build an orbital defense cannon, or they could send a 4 man Xcom squad to become a sleeper cell (perhaps even modifying them to look like aliens/ADVENT), to be activated when the aliens try to launch their weapon. To defend each region from the alien asaults, Xcom can post their own soldiers there. Posting experienced soldiers early lets them train resistance soldiers, supplies lets them build robots and fortifications, while intel increases the chances they'll get the drop on the aliens and produce favorable mission parameters (like starting with all their soldiers and the aliens getting some of theirs as later reinforcements, instead of the other way around).
As a result of this, the avenger/Xcom base itself becomes increasingly resource and manpower strapped, but to compensate the missions don't get that much harder. Then, at some point that can be delayed but not endlessly, the alien assault begins. First, the avenger/headquarters is attacked, as a tutorial to lategame mission structures. Basically each lategame mission is a branching structure of missions, each of which you send 4-8 soldiers out to, which can be Xcom or generic resistance. For the next mission, you send out more troops; if its the same troops they end up wounded and gearless, perhaps even with cooldown abilties gaining limited charges per mission (you're not supposed to run out of soldiers). For the first defense mission, the structure would be that you get attacked at 3 entrances, each of which is a difficult defense mission where you face multiple waves of enemies. If you win you go onto the next entrance. If your troops all die or retreat, you retreat to second line of defense. Once all 3 waves have been fought, if you lost twice against any of them, you fight a last stand against all the surviving aliens with an 8 man squad in bradford's command center. Regardless of whether you win or not, you get to send out the skyranger to reinforce a single region (if you lose, the command staff are onboard with up to the squad limit of surviving soldiers).
Then the next stage begins, where all the alien buffs and non-direct attacks resolve. If you sent sufficient resources to counter them, they get automatically countered otherwise there's a percentage chance. Otherwise you get missions to counter them. And this is where the game gets apocalyptic. The endgame missions are structured so that you can theoretically win with anything, but chances are very high that some of your squads will partially or completely fail, and the lategame mission structures are designed to be dramatic. For example, the WMD strike event could be structured like this. The first mission is a 2 man strike to disable the security around the WMD, with success or death being the only option. If that wins, you make a 4 man attack on the WMD. If that fails, you do a slightly less difficult mission where you go through maintenance ducts or whatever with the surviving 2 soldiers, and then if they make it through that they find the WMD about to activate and they have to choose between aborting the mission, or fighting their way to the weapon and then one of them giving their life to disable it.
Then the next phase is the attacks on regions. Every single region on Earth is attacked by the aliens. If the aliens had preparations for special attacks, some of the attacks are elite units, the rest consist of standard mission units and are thus not that hard to stop. Most of these take standard siege structures ending in either a hopeless last stand or a final sally should you fail the early missions, but some like the Faceless Infiltration might take a more insidious structure that could force you to chose between taking easy missions but the region being devastated, or taking hard missions to protect the population.
Once that's done, the game enters its final phase, which has more of a turn based structure. Each region is divided into human regions that accumulate weak resistance soldiers, or alien controlled/devasted regions that slowly gather an appropriate type of aliens. If Xcom HQ survived, it gets a week to do all the normal upgrading but it can't send out missions. After that, each surviving human region gets to make a simple choice: contribute resources to Xcom HQ (or start a long process of building a new one), upgrade one of its resistance troops into a weak Xcom soldier, or send out its resistance troops/robots/xcom soldiers to attack. This can be liberating a region that isn't too devastated, clearing a region of the gathering aliens, or permanently wiping out one of the alien battalions (any alien unit from one of the region main attack that survived the attack). Xcom HQ can send out the skyranger once during this phase, again if it survived. Everyone else has to use cars or hoof it, meaning they can only attack adjacent regions (although this limitation applies to the aliens as well, and you can transfer infinite distance between connected regions as a free action provided those troops haven't done anything yet). Then, the alien turn begins. First, the aliens send down a new battalion, which either attacks the region if its human held or launches a move/attack if it isn't. Then, all battalions either draw up new troops, or move/attack. Then finally, if any gathering aliens reach a sufficiently large number they form a new battalion, which cannot move. In this phase of the game, multiple Xcom or alien units can move into the same region; this just extends the missions so that everyone involved fights until either one side wins so hard the other retreats, or all of one side is dead.
On the 3rd turn of this, the aliens send down a unit of ethereals/avatars with their bodyguards. Depending on how things are going you get a different theory from the command staff as to why ("they must think they've already won"/"they're trying to turn the tide!"/"they must be truly desperate to risk so much"). There is only one victory condition to the caimpaign: killing these guys. You get a different ending depending on the state of Earth, however: either the aliens scatter and humans regain control of Earth, or the aliens scatter and the last humans live in fear in a post-apocalyptic world were they're no longer the dominant species, alongside a few aliens that joined them out of newfound freewill. If you get the good ending, you get an award cutscene in which all surviving soldiers attend and the soldiers who performed the best are given medals. All participants in the final mission either get a special medal or are honored as heroes. If you get the bad ending, you get multiple different scenes in which the surviving Xcom members (including the command staff and scientists/engineers) are seen huddled around various campfires alongside civilians/soldiers/aliens, discussing the events of the caimpaign. Either way the command staff will comment on the state of Earth and their comments will be better or worse depending how badly the various regions faired. If you score a perfect victory in the first round of attacks (no regions devastated, no regions taken over, Xcom HQ survived), then the aliens will immediately send down their elite unit and you get a special option to send the skyranger to reinforce the attacked region. If you win that battle, you get much the same as the normal good ending, but with an added cutscene explaining one of the game's mysteries in greater detail. All of this is put into a special cutscene that you can not only choose not to watch or delay watching, but save permanently alongside every possible stat on Xcom and its soldiers, in case you want to relive your past victories.
There are only two loss conditions for the entire lategame: all 16 regions lost (even if Xcom HQ is alive), or all Xcom soldiers killed. If all you have is one Xcom soldier in one surviving region, doesn't matter, you can theoretically win by taking out the command unit. Victory or Death!