My pet-peeve with matplotlib is the terrible layout of multiple plots on a grid. It's tedious (requires quite a bit of redundant typing), setting aspect ratios is tricky, getting margins right is an effort of trial and error -- setting reasonable font-sizes will almost certainly get you overlapping axes labels (especially when using tight_layout) by default.

Don't get me wrong matplotlib still gives the best looking publication-ready plots (people mentioned bokeh, which is great for interactive plots on the web, but completely unsuitable for creating plots for pdf articles). I just sometimes wish less tweaking was required.

I found proplot: https://proplot.readthedocs.io/en/stable/ is a nice wrapper around matplotlib that alleviates quite a few issues.