In the Pathfinder DnD campaign I am running things are starting to get complicated in terms of planning. Initially the characters were low level grunts in the army so I could handwave away magic for the most part but now they are level 7 and are extremely influential politically so they could fairly easily requisition whatever spells they need while in their home base. This is problematic because Pathfinder has an absolutely bloody enormous spell list (1300 spells or so) and those spells are really powerful. They can teleport people around, view other people, interview corpses for information, determine the truth of statements, read minds, etc. Setting up a political situation almost always relies on secrets and those are hard to keep when the characters have access to all these spells.
The most difficult thing is that I don't know what all the spells do. I present the characters with a problem and they look through the books and online resources hunting for spells that solve that problem. Last session they found a spell called Cultural Adaptation that let them infiltrate an enemy base in a way I had not anticipated because the spell let them figure out things they could otherwise not know. Cultural Adaptation isn't even a high level spell but it is obscure so I had no idea it existed. I really want to create problems that the characters can solve creatively but it is very difficult to do that when I can't keep a handle on what their capabilities are.
This is one of the issues with games that last a long time and put out a lot of splat material. It is fun for characters to discover new things and explore new options but it is a giant headache for the person trying to plan around all of it. Intrigue and spycraft can make for great adventures but it doesn't work especially well if the players can randomly ignore huge chunks of the scenario. It also doesn't feel like much fun for people to be doing internet searches to figure out what their characters can do all the time. I like people trying to figure out plans based on what is on everybody's character sheet but when clerics in particular can cast any of 750 different spells in a day the other characters feel very left out.
It also feels a bit ridiculous when people realize that their character technically has an ability that would have trivialized a previous encounter that was otherwise exciting. Saying "Well, I really should have cast Win The Game last time, but I guess my character forgot about that... good thing I looked it up online this time!" is a cruddy way to have the game go. I think that magic design really needs to limit the number of different things someone can do. If you can't possibly record all of the stuff your character can do on a few sheets of paper nor keep all of your general capabilities in your head then something is distinctly wrong, both in terms of GMing the game and trying to achieve class balance.