Am I expecting too much too soon from new puppy?

My fiancee and I got a puppy 2 weeks ago. I've never had a puppy but did and continue to do a lot of research as I want to do this right. Given having no background in puppy behavior, I'm curious if I'm expecting too much too soon from our puppy?

She is 12 weeks old, has a crate and a play pen enclosure that is set up in our living room. Although she will sometimes settle herself down and take a nap in the playpen, its not very often. She will bark and whine to be let out to be on the couch with us. We obviously want her to be with us but we also want her to learn how to self regulate and not expect to be with us 24/7. I work a hybrid work schedule and my fiancee works from home. When he is working, her setup is transferred to his office. She cannot be left alone without seeing one of us. Even if we walk into the kitchen (still visible from her setup), she will cry and whine and bark. We really want to avoid any issues with separation anxiety and I'm curious if I'm expecting too much of her too soon and this is normal behavior or if I'm inadvertently causing bad habits?