Things that might be obvious or explained in the prologue (which I skipped) but I only discovered after hours of play:
Tooltips - the panel to the left has tooltips if you mouse over most icons. When presented with three agents to hire, I didn't realize there was anything to differentiate them; then I discovered mousing over an icon on the info panel for each one showed me exactly what traits and associated bonuses they had. Same thing with armies: all active effects are shown when you mouse over the icons in the info panel.
Province Details tab - another easy to miss info panel, the Province Details tab shows you a breakdown of various effects influencing income, unrest, culture etc. along with projected values. Good stuff to know when planning builds.
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