I bet someone else thought about it... I always have seen some clues on something "bigger" going on in Shadows of Amn, so I gathered some clues here and there :
1) Kalah, the tiny little gnome illusionist, mentions in his final breath that he was promised something. He achieved great power in that tent, even though Aerie said his skills weren't ever that powerful. It is possible that he wanted that in his own ambition, as stated that Gnomes are pretty much just made fun of in Athkatla, or hunted down as criminals. But what if his motives weren't his own, but rather he was controlled?
2) In the de'Arnise hold, Glacias, Lord Arnise's personal bodyguard as well as friend states that his new masters shown him the truth through magic. Incidentally, TorGal didn't have ANY magic, but he *did* have some beasts that made holes through the underground - the Umber Hulks!
3) In the dungeon at Windspear hills, we meet Tazok... *again*, even after having him decapitated, splattered in tiny pieces of minced meat... well, you get my meaning. Interestingly enough, he has new masters and new plans this time around and carries a key with him, key that opens a secret door to the sewers in Athkatla!
I am pretty much sure there are other clues scattered around, but I forgot them by today. Yet one thing is certain - all clues lead to the Illithids indirectly. Are those dudes trying to conquer the world or are they simply testing the protagonist? Cut content? Pretty damn sure it was.
What do you guys think?