Ohh my goodness 4th and I am halfway... but I don't think Ill ever have the energy to comment on them all later... MUST GO ON!!!
Standing Guard
-The Fortress guard as we know are the police. The ability to add waypoints allows you to use them as the Military. The same sorta goes with Royal Guards. It is too capable of being abused.
Realign Military:
-Your military moves SLOWLY... At this point I am in the boat where I say it is intentional and your supposed to suppliment their slow movement with Active guards, Guard Dogs, and Traps. It isn't a bug its a feature.
Reload:
-No real arguement here... "Run away and get more ammo" makes perfect sense to me. Though it would take a while.
Seige Warfare:
-Enemies are SCARY and siege opperators are ordinary dwarves... I purpose you just build your Siege engines further back... they got serious range. Besides leaving Siege opperators open to arrow attacks is bad anyhow and I think them running away should be a sign.
Invaders Stuff
-This is going to be SORTA fixed (as you won't get magical Spawning Goblins)... however don't underestimate them, later they have the numbers to uttarly decimate you if it wasn't for the fact that moat and walls PERFECTLY negates them. Your Dwarven Home is impressive especially compared to just about any location.
Militia
-The Fortress guard is a Militia... they just don't alternate.
Fall Back / Rally
-This may very well need to be fixed once you actually get to War on others. Though I think that having limited control rather then the usual absolute control is one of the great features of Dwarf Fortress. "Fall back to behind the traps" may be TOO much control while "Run away" is good.
Citizen Rally Points:
-This is not a bug its a feature. Your not supposed to have hands on control of your citizens... Also your supposed to build in such a way that your citizens are never at the brunt of any attack.
-Side note: There is a "Citizen Rally Point" it is called "Dwarves stay Indoors"