I delayed completing the 3rd Chapter(ending Shadow Thieves quest) until I finished all of my minor quest up to this point. I then started Chapter 4, and man oh man was it short! Did I do something wrong, or were the few minor quest in Brynnlaw and the asylum, all Chapter 4 offers?

The ship captain who brought us to Brynnlaw met me after I "defeated" Jon Irenicus and took Yoshimo's heart. He met me upstairs and told me where to get the key for the mirror and offered, instead, to take me on his ship to Irenicus' location(to cut him off). I "stealthed" past the captain, got the key and am headed for the underdark(which starts Chapter 5), so did I miss something? Should I have gotten back on the ship with the captain? Keep in mind, I want to play every subplot possible.

Thanks Warriors!

You should have talked to Saemon about sailing back, and he would have agreed to take you back on his ship. You then escape with him on a stolen pirate's ship and get waylaid by Githyanki. THIS IS THE ONLY WAY IN WHICH YOU CAN REACH THE SAHUAGIN (OR WHATEVER THE ANNOYING LITTLE BLABBERMOUTHS ARE CALLED)CITY!! I.e. go through the Underdark now and you'll miss out on a subplot!

Yes, you also miss the cloak of cheating. The Sahauguin city is pretty shocking - Sahauguin are weak as piss - but there are several items there that you wouldn't want to miss, as well as a hilarious beholder guarding a chest, which I also wouldn't want to miss.