Both sides certainly have their ups and downs, but it's a fairly simple choice for me. Free Drones, 100%.
The Protectorate/United Cities seem to be a very large and very capable faction, they claim to have the entire Underrail's best interests at heart and the group seems to have some decent people in it. However, their expansionist tendencies, overall disdainful attitude for outsiders (I can imagine a similar attitude towards East and West Underrail too, not just the South) bordering on Jingoism, all of the propaganda, all of the horror stories about them that we've heard from various characters, it all paints a very ugly picture. And then there's the CAU, a bunch of psychotic spooks who make all of the Real- world three letter agencies proud at best and look like the Make-A-Wish foundation at worst. There's also General Malek, who started the Protectorate via the violent overthrow of Reformed Biocorp and who is essentially the de-facto head of the organization as a whole (it's also rumored/implied that he has the final say in any decision made by the United Cities council). To me, the Protectorate looks very much like a military dictatorship disguised as a democracy and will end up doing more harm than good in the long term. And if they gained full control of Underrail and then decided to stop pretending to be nice, would be very difficult to defeat or escape from.
And then there's the Free Drones. Described by people of the protectorate (and some others) as terrorists and bandits. Once you meet them, they come off as decent, reasonable people who value independence and who have very reasonable grievances against the protectorate, given the daunting task of waging a guerrilla war against a huge, well supplied army. Though they have been described from supporters of theirs as having had moments in the past when they let paranoia and fanaticism drive them into going too far. To me, they seems to be a group of scared, bitter and disillusioned people driven to make some hard decisions by circumstance and desperation. And if they did turn bad down the line, they'd be just another warband like the Ironheads and the Grim Jetters, dangerous but neither omnipresent nor invincible.