Note: this post is mainly relevant to eukaryotic flagella, rather than bacterial flagella, which is a whole other topic.
In thrives current state, cilia and flagella function relatively statically. Flagella provide thrust in the direction they point, cilia help rotate. That’s more or less it. To say that this is a very small fraction of what they can do in real life is an understatement.
First, food channeling, probably one of if not the biggest usage of cilia in real life, is totally absent. This method of eating is common, in both single and multicellular organisms, such as with a central mouth in peritrichs or rotifers, or an oral groove in many other cilliates. Flagella are capable of many more things than just thrust away from them too. In dinoflagellates, they are much more complicated than just pushing in one direction, can push in directions other than where they are facing of of the cell, and look a lot prettier too. Flagella arent all the same in structure either, some of the flagella have tiny structures on called flagellar hairs which impact how they behave and cause motion, and flagella can be different lengths, there is a lot of variation.
some examples, all own (mediocre) work
Example of dinoflagellate transverse flagella being mesmerizing. (slowed down ~55x from real time)
Example of cilia on a random cilliate, also slowed from real time
So, basically, I hope that in the future cilia and flagella basically get the ability to be configured to do different stuff, behave in different ways, and have different features, as they feel quite limited in their current state. I do of course understand that by nature, thrive has to be limited in organelle options to remain practical, but changes such as being able to direct the thrust of cilia and flagella, aswell as making them have impacts on cells and other objects in the environment, would be a change that I would love to see in the game’s future, as it would open up a lot more options for organism design.