If we're just going to suggest plot stuff then I'd like to suggest the following:
Have the appearance, nature and behavior of the Trespassers reflect the war effort. If the war effort's losing or just getting started, then the Trespassers should basically be upstarts. The weak, who, through consuming the denizens of the frontier worlds, have grown stronger. Basically, what's currently being fought: entities that clearly resemble what they mimic in both appearance, capabilities and behavior.
However, as the campaign drags on, and assuming the defenders are actually winning, the Trespassers should slowly change, as the upstarts are destroyed and the more powerful ones begin to starve as their intrusions are pushed back. Eventually, the party should no longer be fighting bosses (regulars foes are still fine) that just take a form appropriate to a world but rather ones who do not. Ones who, in another time could have devoured entire worlds without a thought, who would rend apart deities as if they were mere insects, whose very presences made reality unravel. The emaciated husks of old gods, dangerous but mere shadows of what they once were, starved by set back after set back. They should, if anything recognizable even remains, be based on the fallen figures of universes that no longer exist, or amalgamations of numerous battle-torn worlds.
They should be still powerful enough to put up a fight (and certainly not easier than their predecessors), yet weakened enough that their wretched state becomes known. Perhaps, every now and then they'll try to use some sort of attack, something that they could cast with the merest thought before but which they are far too weak to use now; perhaps they'll start suffering from fear effects, sometimes even covering for reasons they cannot even understand as residual instincts from their assimilated prey screaming at them to run; or perhaps they'll just be broken, already in a critical state by the time the battle even begins yet still having more health than those who came before. The battles should focus more and more on exploiting their weaknesses, rather than focusing on the party's strengths, more on stamping out a great threat that still has a chance to regain its former glory, than on repelling growing intruders.
This is for a few reasons, firstly, it'll bring something new to the table after everyone's figured out how to use their characters in tandem, what the optimal action sequences are and whatnot. It'll force them to think on their feet again, to win battles based more on chiseling away at the cracks in their foe's armor than on just smashing them apart with overwhelming force. Secondly, it gives a sense of progress, that circumstances are changing, that their actions matter. It goes from fighting the familiar to fighting the unknown, foes from settings that might not even resemble any particularly well known piece of fiction, or which are gestalt entities.
Lastly, and perhaps most importantly, it gives a sense of accomplishment. Often in films, it is in the darkest hour whereupon victory is snatched, yet this doesn't leave players in a game feeling too accomplished, for even fools have their rare strokes of brilliance, and tragic figures their moments of fortune. No, by slowly and systematically crushing your foe, by seeing as their ranks fall apart revealing the starved remnants of those who could once erase entire worlds, that is a far more profound sense of accomplishment.
Knowing that it isn't because you won here or there, but rather because you won and kept on winning, that your foe could've recovered yet you're still forcing them back. There'd still be tension, for you will know that in the beginning you too were on the brink, and that your foe may recover just the same should you fail. But also perhaps even more compelling, living on the knife's edge for so long dulls it, to stand beneath the Sword of Damocles day in day out brews apathy. Here, you're not fighting for the same reason of "because otherwise everyone dies" every single time, you'll be fighting to ensure your recent victories were not in vain, fighting to keep the ground you only just earned, fighting because your actions made a difference and you'll see that change through.
And in the end, to face monstrosities that were once too terrible to even comprehend; to prevail in hard-fought battles against them yet knowing that compared to all the stories, they were disappointments; to perhaps even in the briefest moments in the those sleepless nights to feel pity for them; that is when you feel like you're winning. To know that you've ruined your foes so thoroughly, that you've hurled from the loftiest heights of grace, that you've made them reel from your onslaughts, that's when you feel like you've accomplished something truly impressive.