Congratulations for completing your playthrough!
Aside from the pokedex sidequest (which is connected to starter egg quest and restoration projects - both available in the Grand Hall), i sugget you try your skill and patience with magic square puzzle if you haven't already. You can start it in the house in Agate City next to the pokemon center. Though I think by doing the pokedex quest you'll stumble upon the majority of the sidequests.
As for the leaders, i can't remember every one of them but Shade and Noel posed a problem for me. Samson, Charlotte and Terra (90% bc of garchomp) were also diffucult and i certainly didn't win on the first try. Trick room + rampardos/araquanid helped a lot in these gyms. Similarly to you i was prepared the most for Titania and the battle was still challenging. I remember fighting Amy in doubles since i wanted to beat her at her best. Hardy was meh. Now that i think about it, some of those battles were difficult because i barely used any healing items, usually as many as the specific leader had or less.
Eventually, you can always start a new playthrough and do a mono-run or explore various story branches. Perhaps you'll get different ending when ep19 comes out, who knows?