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.
Why does plugging in FFTA into the GBA side give you the Libra ability? Because Libra reveals traps, which were never part of Tactics Advance, and thus the game is giving returning players a chance to react to an entirely new gimmick.
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.