Just wait till he has to match and you'll be expected to quit your job and pick up and move with him! J/K. Well, not really... but you just have to put it into perspective.
I think that you need to communicate with your SO more. Many years ago I told my FH that I felt like he just discounted both my education and later my career when he would ask me to stay home to wait for the electrician while he went to study at the library or something. That would p!ss me off to no end. So I finally told him that my education was not any less important than his (I was getting an MBA) and that if he wanted at least one of us to get a job (since he had many years of med school left at that point), then he better make his schedule more accomodating for the electrician or whatever. That was the end of that. He never asked me to stay home from school or work again.
Then again, sometimes our plans get shot bc he has to do emergency surgery or something. So in those instances, yes your relationship gets put on the back burner. Sometimes we can't plan weekends away bc he is on call or needs to study or something. But that's what a career in medicine entails. And you have to choose whether or not you can accept that.
Now we're in the process of matching and we're faced with the possibility of having to pick up and move with very little notice. I might have to quit my job and find a new one, while also finding an apt in a new city and arranging our move (bc I already know he will not have the time or inclination to do this). For a while I felt like I was getting sidelined and just "expected" to follow him, but then he asked me what I wanted to do and if I would be willing to take that hit to my career. I have to admit that this has taken the edge off the prospective.
So the short answer to your question is yes, I think that most medical partners do, at some point, feel like they are in second-place, but if you communicate well with your other half, you can make things work out to a point at which they are acceptable to both of you.
GL!