I am not sure if this is the correct category to put this in. I notice that there was no discussion on peopleβs favorite versions of Thrive. Specifically, for Beta, Alpha, and Sub-Alpha/bugfix versions. Beta versions are less than 1.0.0.0., like 0.8.0.0. Alpha versions would be the third digit, such as 0.8.2.0. Sub-Alphas/bugfix versions are the fourth, or last digit, like 0.8.2.1. Unless I am mixing up how Thrive uses terminology for official releases, since there are Beta and Alpha versions of updates before they are officially released. Here is a list of all the Thrive releases so far in Github, as well as some on the Thrive Wiki, which has legacy versions before 0.2.3.0.
For me, it is hard to say. 0.6.3.0 was the first version I played of Thrive. This was the before the massive speed reduction due to size implemented in 0.6.4.0, so I could witness massive 200+ hex cells that move faster than you think in the game. This was a result of that version of Thrive having a max mutation rate of 5. I am not sure when this was reduced to 3?[1]
On the other hand, I loved the Injectisome upgrade for Pilus in 0.6.4.0. I also liked the Endosymbiosis feature added in 0.6.7.0., despite how extremely challenging it can be to complete this. And the different Toxins, along with the Mucocyst upgrade for the Slime Jet, in 0.7.0.0. Or Hydrogenase in 0.7.1, which has become one of my main go-to organelles. I could keep on listing things, honestly. 
Maybe 0.7.0.0? β©οΈ