Here's how I avoid both of those situations:
First, I cannot say enough good things about Liz Lange maternity tank tops from Target. They're basically a long, butt-covering version of the great $12 cotton tanks that you usually get. There is no ruching on the sides and the cut hasn't been changed otherwise, which makes them perfect for pulling off the leggings and boots look when you shirt or sweater isn't quite long enough to cover everything it should (because leggings are not pants!!)
Second, don't get me wrong, I am not saying that regular jeans don't go with flannel. I wear it too, but the lighter the jean and the more casual the shoe makes the outfit start to feel rustic. However, swapping your normal jeans for black denim and a ballet flat with some edge (or not) and a cute clutch makes the flannel feel more chic and on-trend.
Still need a flannel shirt? Here are some affordable options:
What's your favorite way to wear flannel?