I honestly can't remember what I thought when I first played through ToB...though I suppose it's pretty obvious Melissan is up to no good.
Both SoA's and ToB's main plots are pretty weak though if you ask me.

I can't say that I "figured out the plot" exactly, but I knew that she wasn't who she seemed to be: who is this person who knows CHARNAME (by name) and all the other Bhaalspawn? Why is this person rounding them up to 'protect' them? Who are you? "Can't tell you." Why are you doing this? "Can't tell you". Yeah, right!

Those were my thoughts exactly. When I learned that she brought the Bhaalspawn here to "protect" them, I was like "Yeah sure. And you did not even consider the fact that maybe, just maybe this makes them easier to kill all at once?"
And she seemed to be surprised by the fact that the town is attacked. Yeah, sure, she could not possibly see this coming.... Nobody is THIS much of an idiot.
Oh, and after the siege is over, I meet her OUTSIDE. WITHOUT A SCRATCH ON HER.
I wanted to attack and kill her on the spot, but there was no such option. Appearantly my CHARNAME is a moron -_-

ToB writing sucked. Loved Watcher's Keep and the fights, but nothing can save the plot :(

Easy to figure out. From the greaseball magotty dialogue of hers with Gromnir, i immediately figured her out. Typical villain woman; sowing chaos and discord, then psychologically torturing the insecure, half-mad man in power (she even reminded me of my ex or something)... And in the name of "what's good for people" and "i want justice, equality, to help a good cause" cr@p. I know my sh*t; each and every time even the tiniest hint of those themes can be sniffed in the air, the source emanating them is 99% a troublemaker villain who wants to make a mess and innocents suffer out of it as an outcome (instead of being "helped").