They had big ideas for it, but as time went on the budget got squeezed while needing more CGI on screen to represent the advanced technology and galactic stage they were portraying.
The actors started to cost more too. One of the reasons why many shows are limited to 5 seasons is that the standard contract is 5 seasons and then a re-negotiation for more money. Amazon has another trick that they used with Bosch - can the show, and start an identical one with the same characters and actors, but a slightly different name and a big reset of everyone's salaries.
It's a real shame that Universe was cancelled. Lots of potential and an interesting idea.
Maybe Amazon isn't the right place for it though. Look at the final season of The Boys. Massive budget cuts were very apparent.