There's basically no avoiding the concept of a "doomstack". One way or another, you're going to have to "bring everything you've got" to smash down a particularly defended area.
However I found that splitting my fleet is a good choice against empires that focus on a doomstack. A doomstack can't be in two places at once, it has to split. So by having sensor coverage - so that you know where there aren't any defenses - and maintaining a group of smaller fleets you can tie up the enemy's doomstack pretty well. At that point it's just a matter of having enough firepower to wreck his static defenses and infrastructure, and bombarding those of his planets he can't protect to deny him resource income.
In realistic terms, there's really only one real problem with pooling all your armies together. The larger a force is, the harder it is to manage and coordinate. You could introduce a fleet size penalty to naval capacity, necessitating the creation of a number of smaller fleets instead of large groups if you want to maximize your total fleet power. Experience level and traits of the admiral in command of the fleet, would affect the cutoff point of the cap, allowing the admiral to command larger fleets without drawing extra naval capacity. Empire leader capacity and influence income would then naturally limit the number of fleets you can have at the same time, as leaderless fleets would start going over nominal capacity values very quickly.
This wouldn't really "solve" the doomstack problem, as the doomstack would still exist, albeit in smaller chunks. But it'd put a definite cap on how large an empire's fleets can grow.
A good addition to go along with such a change, would be monitor fleets.
Right now static defenses are really, really dumb. They're not going to get much better post-1.9, because just the sheer idea that a station can defend an area of space is ridiculous. There will always need to be a fleet.
Small problem with that is, empire naval capacity isn't unlimited. You can't build defensive fleets as freely as you can stations (and that's saying something considering how restricted military station placement is).
But, what if you could actually have a meaningful use for monitors? You can already build them, even though there's no worldly reason why you would deny a ship interstellar capacity to save a meager 5 minerals.
But you could, say, introduce some Spaceport modules (and later, Starbase modules?) that give a colony/starbase the ability to support a certain amount of naval assets. Have that be subject to expansion, with nav-cap techs, scaling with spaceport/starbase level, maybe colony pop size or colony structures.
Then, as long as it's that spaceport or starbase building the ships (because they're monitors, obviously), you could have a fairly significant amount of mobile firepower stationed within the system,
without affecting your overall naval cap. It would alleviate some doomstack problems (as in-system defenses could be both larger, letting the defender operate a smaller defense fleet, and would be subject to attrition, unlike a space station that can only be destroyed all at once and can be repaired way too quickly), and... I guess bring the game even closer to Dominions. Province Defense!