I played around a bit and it's all very overwhelming, but in a good way! I play with Kyle Skye, a fighter, and Aileya Skye, sort of a priestess (enchantress with earth magic instead of air).
I just met Arhu who said something like "my name is Arhu" and I was like "no, that's
my name" and then it hit me: I was talking to my self. ... Epiphanic moment.
Yes, I'm well aware that my third option would be to simply choose the dialogue responses for the companion. I have no desire to do that though.
I had the same fear about having to roleplay two characters at the same time — wouldn't that feel schizophrenic? But in practice it turned out to be quite alright and fun, too. I even learned stuff about my two protagonists I didn't know before!
Case in point: I created Kyle as a typical brute and Aileya as a charismatic and affectionate healer. Now they read a note in the starting area about a guy who died after jumping from a cliff because he believed in something. Kyle and Aileya talked about it — that is to say, I decided on how they would reply, — and as it turned out, Kyle is actually a romantic (bonus on luck) while Aileya has a pragmatic view on things (bonus on crafting). In retrospect it fits perfectly and the image I have of my two heroes was refined in the process. I'm loving it!
If you sort of know how your characters should be like, choosing replies is fairly easy and feels rewarding in its own way.