I have been re-thinking this lately. The current concept is something along the lines of Belvoir Fortress (Star of the Jordan) in terms of size and architecture: a mid-sized castle on a mid-sized and somewhat steep hill, possibly with a hamlet on one side of the hill and a small swampy lake (unlike Belvoir which is 12 miles from the nearest significant body of water - the Sea of the Galilee) on the other side.
The castle's dungeons and the hamlet's older buildings - such as smithy and temple - connect to the dungeon, and so does the swampy lake - there is at least one half-flooded sub-level.
There should be a cult in the hamlet, with its "priests" actually being Mages trained by the Aboleth, who has significant arcane knowledge.
No sewer and not many thieves, but cultists, undead - and lizardmen. The lizardman may or may not be under the Aboleth's influence, though I do like the idea of them receiving advice and organization from the "Deep God" - PCs expecting primitive lizards find a well-organized micro-civilization built on the ancient abomination's advice.