I tend not to specifically target my players skills, rather I set up an encounter or obstacle and it is up to the players to look at their skills and abilities to figure out how to defeat or bypass it. It's probably why I don't really worry about flying PCs, and wouldn't make any changes to something like Tomb of Annihilation. I'm running some old Thunder Rift modules and haven't changed a thing (unless something, normally a monster, doesn't exist in 5e, then I might make a replacement). One of the players is playing a homebrewed pixie that can fly and turn invisible, he'll often scout out a large portion of the dungeons, but the thing is, the players still have to get through the dungeon.
With homebrewed adventures, the only things I specifically tailor to my players are items that might be useful and fun for their class. I don't do this for all items, but just enough that each player ends up with something. For the Thunder Rift modules though, I just throw in whatever the modules have. Players are getting a heap of items and treasure, I'd almost forgotten how much these modules gave out, but then considering how deadly they are, I guess you kind of need them.