So, I'm playing this cleric/thief who (RP-wise) reveres Tymora. With that in mind, I'm leaning towards the thief stronghold. It probably wouldn't make sense to do the cleric stronghold line and come out of it with a symbol of a god my character doesn't worship. Whereas the thieves' guild is slightly more plot integral (though unfortunately more high maintenance).
Alignment-wise, I'm on the cusp of CG and CN, but I'm really not sure where I fall. I figure I have these going for/against each:
CG: It's basically a "good" run and I am kinda becoming the hero of the region. I virtually always take the "good" options in dialogues and quests. I save and protect others. I put myself at risk for the party's sake when I could send someone else in to take the risk for me.
CN: I walk into people's houses I don't really know and chat them up (Town Councilman in Beregost, Joseph's Wife in Nashkel, Firebead in Beregost, etc.) I "explore" their houses as well, and if they have something that may be useful for my "noble" journey, I commandeer it for the cause. Sanctuary has become Rob-People-And-Get-Away-With-It. The thieves guild is basically the fantasy equivalent of the mob.
So, the specifics seem CN to me, but the overarching theme seems CG.