This troper had one concerning the Art of the characters. In FFTA many of the characters looked childish and young, while in this game, FFTA 2, the characters looked older, more mature, with more realistic art. The brilliance comes into play with how the main characters got to Ivalice: In the first game, Ivalice was simply a fake world from their imagination brought to life, and they were 12 year old kids. Obviously everyone would look more childish! while in FFTA 2, where it is THE REAL Ivalice, they would look more realistic due to being actual people and not created from a mystical beings power! (could just be art evolution, but this is how I figured the difference in art was)
The "Of Kupos and Cannons" mission is pretty brilliant. While you're fighting the Moogles, they seem to be using the wells in an area they had made into a weapons testing ground as a Clown Car Base. Later, you have an optional mission that requires you to examine the wells. Doing so reveals that the wells are actually portals to locations across the sea, two of which are relatively close to a city built by Moogles.
In Final Fantasy Tactics A2, there is the mission "I Want To Forget". The client has decided that he can no longer live with the pain he feels for his unrequited love ("I love someone that I can never have") and has requested that your clan get him zombie powder so that he can quit his mortal life. Long story short, you are given a choice between fulfilling the obligations of your quest by getting him zombie powder, or to instead get him lethean draught so he can simply forget his love and his pain. The subtle horror comes if you paid attention to how zombie powder works. The user dies and becomes a walking corpse... and their memories are preserved. If your client were to take zombie powder, he would not forget the love or be released from his pain. He would instead be a near-immortal walking corpse that remembers all of it.
As you get to see later in the Duelhorn saga, the results of the other option, the Lethean drought aren't too pretty either.