Okay I'm trying to get down all of the changes to the stat stuff.
I notice that you can now raise your stat as well as an S link's level at the same time. I decided to study in the library with Chie, thus raising my knowledge stat and her giving way to leveling her up. A really good time saver.
There's also the fridge, which occasionally has old food. Eating it raises your courage.
On rainy days, go to Aiya and pay 3000 yen for their competition. You may not have what it takes to win the competition, but doing this raises a multitude of various stats all at once. Awesome
You can even raise your stats in mid conversation if you pick certain dialogue choices.
I'm in a rush to get Knowledge to Expert level so I can do Margaret's Quests right now.