The series of updates Toady planned would each break save compatiblity. To make things easier, he did it all at once. There should be a more rapid release schedule. We're already on the 2nd bugfix release.
My suggestion does not require breaking savegame compatibility with future versions. You could include all the same savegame infrastructure, and just not use the parts that relate to currently nonfunctional systems.
I feel the need to poke you here. YOU have no idea how save games are written. To say he could make all the changes he has, and not break it once if he released slowly, is I don't even know. Yes, he could have released each section as he was done with it, possibly in the course of a week, possibly a month. Each time he released, it would break the previous versions saves. You would have had a year with constantly changing games, and no consistency. Oh, and lets not forget that the 40d# series would never have been worked on.
As for the old military system working, it didn't. It was almost a hack to let you kill things, not the end system. As a method to arm your dwarves and tell them to stand around, it worked wonders. To actually have a functioning military, with training, patrolling, and off duty scheduling, it could never have handled that.
The others, wardogs, traps, and marksdwarves, meh. The game is 31% done. I wouldn't be surprised if at 1.00 donkeys were the prominent defense strategy. Guess what, cage traps are still unbeatable. You can still build your ivory tower, and fling gobbos off of it. In fact, you can make your tower OUT OF IVORY without hacks now. Or goblin bone.
To sum it up, you are an ALPHA tester. You take the product you are handed, and mercilessly dissect it to find bugs and improvements. You don't have any real say in where it goes though. If Toady decides to make this an FPS, more power to him. It's HIS choice, you are merely here to test what he gives you to test.