I like the shallows that your map now has Talroth, it adds a little extra pizzaz to the map.
I know you are trying to avoid the computer generated "CC2look" with your map in favor of something that appears hand drawn, but the color palette you are using right now (dark brown and purple) looks synthetic and processed (not that that's a bad thing, there are many digital maps, especially by cartographers like Christopher West and keith Curtis I am quite fond of).
If you are going for a more "hand drawn" look, there are several options you can use. You can go with bright primary colors on a white background. Or you can go with the "aged parchment" look for the background to your map (I'll see if I can find a tutorial on the guild, I know there's been one). It really all depends on what type of look you want. Medieval maps tended to be more artistic than functional, showing buildings and landmarks rather than blocks and street grid. Your map seems to be more on the functional side, so anachronistically, you might want to look at 18th and 19th century city maps.
Also, is the terrain your city is on or near similar to northern France, Holland, and Germany or Greece (meaning do you have fertile plains and forest covered lands around the city or high cliffs of granite and bedrock)? If the terrain is more akin to northern Europe, then your harbor looks off. The sea opening (or openings) to the harbor would be wider do to tidal action and erosion. If the terrain is more akin to Greece, than the shape looks right, but I doubt you'd have a marsh nearby. I actually thought the shape of your first map looked better/more natural.
As for the Temple of the Six, is it the only religion in your Kingdom or are other religions (albeit grudgingly) permitted? If so, if might be smart to have a temple quarter. If not, given that you say six is an important number to the faith, then in a city the size you are depicting, you should have one main temple and five smaller shrines--I counted three in the initial map all told.
Although its was created for a sci-fi setting, I find Zierra in another thread here on the guild an interesting contrast to your map. It's your call whether or not you want to include piers, but I do think they add a bit or realism/versimilitude to aeronox's port city. I also like the fact that the road grid is denser in the oldest part of his city (which I assume is the west side) reflecting the greater buildup and competition for land over time.
I like your concepts of walls with moats/canals. Not only is it defensible, but it clearly delineates where the protected sections of your city are. I would have a walled bastion/fort or two as a place for a last stand during a siege or a base to reestablish control from during riots.
Keep refining your concept Talroth. What you have is very promising, I'm curious how it turns out in further iterations.