Don't argue for the removal of doomstacks unless you have a good alternative for how wars should be won. As is, it's perfectly reasonable that the larger empire with the larger fleet always wins, because there isn't any other good reason for an empire to win the war.
And even after a change, an empire's advantage in a war should directly scale with their size advantage, there should just be more ways to make up a 10-20% fleet gap with clever strategy. You should never be able to reliably defeat an empire twice your size without help.
EDIT: It's only right that I discuss my own alternative.
The problem with Stellaris is the same as in every other Paradox series except Hearts of Iron - the scale of the game means that you can't represent anything below the level of strategic maneuvering, and all battles have to be resolved by dice roll. This means that the only things that decide a battle are which dice roll modifiers you have going into it - better numbers, better tech, and in most games terrain also. Even the strategic movement of troops is usually a trivial decision because of the level of detail of the games, strategy is reduced to either avoiding or hunting down enemy armies depending on your dice modifier advantage, and capturing static locations by sitting on them long enough.
So, military competition in every Paradox game (except HoI) is primarily about the investments you make into your military before a war even begins. It's about making sure that when the fighting starts, you have more dice modifiers - essentially it's like some traditional RPGs, where the focus is entirely on building your character, and combat is entirely decided by the stats and spells and abilities you've chosen to upgrade, not skill.
So what does this have to do with doomstacks in Stellaris? Well... it means I don't really view it as a problem. The power of your doomstack is a direct result of your investments of resources into research, expansion, and construction. If you've handled that part of the game better than your opponent, you should win.
The way to make warfare interesting isn't to subvert this mechanic by adding in RTS-like elements of personal control over armies and ships. It's to give us interesting and viable alternative investments of resources that affect strategy in different ways.
For example, focusing heavily on defensive stations and related techs instead of a powerful offensive fleet, which could give you disproportionate total combat power for your size, but meaning that a great deal of that combat power is barred from offensive actions. In game terms, this could mean buffing forts and/or letting them be built adjacently, but making them take up precious fleet cap.
Or, if you're an especially small power that is the part of a large federation (which should be the only reliable way of surviving into the late game as a small empire), you could have several interesting choices in how to specialize your military - make your planets and star systems porcupines that aren't worth the effort it takes to assault, while you invest heavily in research to buff the federation fleet; with the addition of trade, commerce raiding could become a thing (although it should be largely automated, so no tedious chasing down of individual corvettes with your own corvettes); build the scariest offensive armies possible, so that federation fleets can move from planet to planet as fast as possible; or, just invest in the best fleet your empire can build, and contribute to the main combat force of the federation.
But, ultimately, we can't escape from the fact that when two doomstacks meet, the larger one should win, and that's a fundamental feature of the game that shouldn't be changed.
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