Thanks!
I first have the animation idea brew in my head for about 2 weeks, so I know exactly what scenes there will be. Then it's just a combination of Inkscape, Synfig Studio and Kdenlive.
For each scene, I first create a static version (i.e. vector art) on Inkscape. Then I import it into Synfig Studio for making vector animation. Finally I put all the snippets together and add sound in Kdenlive.