They're both the same thing, only difference is the new graphics, soundtrack and steam workshop, so It's going to depend mainly on whether you want to play with ASCII or not. Keep in mind that v50 (current version) is lacking some community made utilities and no custom tilesets were ported over as of yet, so if you want to use them you'd have to play v47 (pre-steam version) but you'd be missing out on the new UI and controls which are both a massive improvement. Honestly, the paid version would be easier to learn just because you wouldn't need to decipher the ASCII, but if that's not a problem go with the free version first.
I've very slowly gotten over the old muscle memory. For a while I hoped they'd be able to get the same configuration, but I'm not sure that's technically possible from what I've heard. It doesn't really bother me much anymore even though I loved it being all keyboard.
Rambling aside, are there not any mechanical updates that diverge from v47 yet? Obviously there's been a lot of work getting adventure mode and graphics up to snuff, but I thought some sort of minor changes were made along the way. Even what I'm thinking, or likely imagining, would be pedantic differences, though.
I think there's some very minor mechanical differences, mostly relating to the new UI and bug fixes/new bugs, but nothing major. My understanding is that they planned on finishing the villains stuff after the adventure update.
I didn't play much myself, but I believe one thing can be said: if you don't like keyboard-heavy controls, go for the steam version
It has a more modern UI and graphics, even though you could get some of the features (or all of them), you'd need to spend some time setting up thr mods