As long and tedious as this game series may have been the best thing I have found added wa the directions to complete a story of tasks.

wa? I only just realized, after writing up my entire reply, that you meant was.

The most confusing is investigations

Interestingly, when viewing it in Japanese the label is "Free". Edit: no, wait, that's optional...

I think it's just to separate it from the "assigned" quests, but I'm not really sure.

Next is the new locations. These seem to cover new villages, new maps to hunt and few other things.

Ah, are there actually new villages? I haven't been to any yet.

As basic as the maps are they do not give all the details like when a wall is one directional and where caves or crawl spaces may have entrances.

Yeah, sometimes while hunting stuff in that first area I can't tell if they've gone up the tree or down under.

Have you figured out how to tell the scout flies to go after a specific target? It took me forever... you do it from the map view, by selecting the monster name and ... oh man, what was it, hit X? This made it a lot easier navigating the ups and downs trying to get back to a monster after having feinted.