I'm a newbie reader and often find myself needing to open the dictionary at least once every few pages. Although I'm a newbie, my vocabulary is at least of an average proficiency so I wonder what it's like for the majority of readers, how much does the average reader care about vocabulary? Do you need to be careful not to use uncommon words so as not to break the flow of a reader? Or maybe you need to decide on your target audience and try to find the appropriate vocabulary for them? How do authors choose their vocabulary?
Write for your audience plus a little.
If you're writing a book for five-year-olds, you don't want to use "sesquipedalian," but there's nothing wrong with "lengthy." Part of how we expand our vocabularies is by seeing new words in context (and looking them up if we have to). I remember learning guerdon (a reward or gift) and gravid (pregnant) from Anne McCaffrey novels.
You are correct in thinking that too many unusual words may break the reader's flow, so unless it's jargon (all the various terms for horse accessories or armor, for example), try not to overdo it. But the occasional stretch word is a good thing.
have you ever read the series of unfortunate events by lemony snicket? in those books, the author uses an abundance of long and complicated words that many children wont understand, however, he explains many of them with examples relating to the story. your choice of vocabulary depends a lot on your targeted audience. if you are writing for your own age group, use vocabulary that you yourself enjoy reading and the vocabulary that comes to you naturally. personally, i enjoy reading books that have a slightly harder vocabulary. it makes it more challenging, interesting and engaging. likewise, when i'm writing, i find myself using the thesaurus a lot to add a little more spice to my work.
Prose should slide off your fingers like warm butter. If your brain screams "discombobulated" at you, you don't have to ignore it because it's a big word. There is of course a limit based on your working vocabulary and the genre. Too many big words is snooty.
I became a much better writer when I stopped using a thesaurus. My dictionary primarily gets used for parts of speech and hyphenation; however, my spelling's not great, but I use Word so it tells me.