To a certain extent the negativity is predictable. People do not generally like change... especially change that can be perceived as "subtracting" rather than additive.
Retribution mostly "adds" by first subtracting. In order to "add" cargo ships that would make sense and be useful and further justify HyperGates as a early-game tech/etc. they needed to "Subtract" production. They chose to do so by subtracting the population growth that created that production.
Many buildings and features also became "subtracted" such as the limiting of the "Aid Technology" ability to only the tech capital, or the training of legions. Ultimately, in today's audience, re-balancing in this manner is poorly received. Add to this, that unlike a competitive multiplayer game, where the quest for "balance" is always regarded as "good" or necessary... that is much less present in a single player game in my experience.
The tech tree is another example, you can find many complaints that simply state "the tech tree is smaller". There is a bias for "more" even when more is not necessarily better.
And GC3 has a pretty terrible history of repeatedly subtracting. All of it IS creating a more coherent design (which even if I'm not the biggest fan of, I approve of coherency). Removing the so-called Economic Wheel, removing the continual projects, removing the many different buildings and replacing them with "one off" buildings/versions, removing civ specific tech trees (and moving some of their unique techs into various abilities).... all BUT removing Minor Races.
Fair or not... it leaves a lot of players with a bad taste. Their mentally exhausted with keeping up with the changes and rehashing of the game. Then on top of that, the design direction is definitely no longer "typical" of what fans of classic 4X would look for. More and more the game is pushing for "distinct choice" and for limitations.
That means the game relies on Mercenaries, Citizens, Government rewarded ships, etc., Unique buildings, to meet the needs of the game/player/winning... instead of on more scalable, less specific/discreet items.
Prior to Legions, one only needed transports and population for armies... then we limited it to legions... which you COULD manufacture, but you mostly needed Generals to spawn them, then with this last update, your limited to producing legions from a single planet, further forcing you to make your citizen choices be generals/difficult choices.
I'm not saying this is a bad thing. I'm just trying to showcase, that it isn't typical and it's a change. If all the changes were simply layering on top of the existing game and not rebalancing, you wouldn't have nearly so much push-back.