How to change the main weapons (swords)? Press 1/2/3 from your keyboard. An option is for swords, one for those attached daggers and one for fists.
How to select the second weapons/tools (pistols/smoke bomb etc)? You can use mouse scroll up and down.
Always run without having to keep shift pressed? Check this article.
Skip cutscenes? You can’t.
Gold and resources. You can get gold from plundering ships and selling the cargo (rum, sugar etc, mats that are not required to upgrade your ship). Also from treasure chests, assassination quests, animal skins etc.
More tips and tricks
You can change and check the controls of your ship from the main menu. For example, mortars are triggered by pressing the “q” button.
Other attacks for your ship: side cannons, front attack (shoot some bombs) and rear attack (fire barrels).
You can use the fast travel feature. Press TAB to open the map and click on an icon (a city or a place that you have already visited) > press control to use fast travel to that location.
From your ship, press “e” and scroll wheel up to investigate enemy ships. You can see what resources you can plunder from them. The big (high level) ships are usually transporting metal, an important resource for upgrading your ship. You might have to farm metal and other resources to upgrade your ship in order to pass some missions that are involving naval combat.
If you have other tips and tricks, please share them in the comments.