What is the spirit of the game? Isn't it to build fortresses? If I asked "What is the spirit of the game" on this forum, how many different answers do you think I'd get?
This really isn't rocket science.
Things start hidden. This isn't regarded as a bug. (Feel free to start your own bug entry if you disagree.) In fact many features(trees, forgotten beats, HFS)
depend on things being revealed by your activities and would break if everything started revealed.
Therefore this is intended, and isn't likely to be modified just to fit
your preferences over the designers'.
This really isn't rocket science.
I am not advocating a major gameplay change, but for options that already exist - albeit annoyingly fiddly - to be included in the game so that these options are there and they are stable, up-to-date and don't require switching between programs or downloading a folder full of random utilites.
You're asking for an enormous amount of work to be done in order to please pretty much you alone. It's not trivial to just "include" other programs in your own, if this was done it'd pretty much mean building their own version from scratch.
It doesn't have to be in an in-game menu.
Then why does it need to be in-game at all? Why aren't you bitching at the makers of the third-party utilities for making them so difficult to use? Certainly they could be doing a better job, too, and may actually be more likely to take your suggestions than a game that's intentionally built not the way you want it.
P.S: I'd also add reasons like 'usability' and 'stability' as reasons Toady wouldn't have released the arena earlier. It's got a fairly nice interface right now, probably much nicer than the one he used. Given compiler-powers, much fewer menu options would be needed to test things with it.