A lot of the issues with Menaan are probably because, as unfortunately in other cases, I didn't finish detailing the exterior.
1. I suppose the gaps should be made either narrower or wide enough to allow people to pass. For the first one, I'd probably just patch up the hole with planks to close of the yard behind it. That said, I never finished detailing Menaan, and from the texture seam there I was probably planning to put rocks or something over there to block the gap.
2. the doors that can't be reached are not supposed to be reached via the exterior; they lead from the interior into the yard of the manor. I do think the large rock in the town center could be scaled down and moved out of the way to open things up a little, at least. Or removed entirely. The yard, however, should stay.
3. I don't really like the idea of placing a building in the center of the town, and am not sure what that's supposed to achieve.
4. the gate at the siltstrider is intended as a rough barricade against the bandits, erected by the people living in those two houses. I was probably intending to extend that rough barricade to cover the gap next to it, but it's supposed to be a pitiful makeshift thing.
5. the walls are intended largely to discourage bandits and wild animals, not withstand a full-blown siege. Even so, while players can leap over the walls elsewhere, an attacking force could not effectively do so. Not to mention that there's a lot of vanilla (and real-world) precedent for not entirely effective walls.

Edit: right, and the towers are not purely there to block access into the town, in which case they would indeed be excessive considering the rest of the wall. They are essentially the 'keep' or last refuge of the town, where the townspeople and their most important goods would retreat to in the unlikely case of a larger attack. But large attacks aren't really a concern there; for the most part, the occasional thieves and wild animals are the only real threat, and the towers serve more as watchtowers than anything else.