The biggest problem I've had is that Flail/Whip/Scourge is insanely overpowered at the moment. I've seen another thread where it mentions that the attack power is concentrated into the weapon's area of impact. Since these weapons are defined as having a very small area of impact, they hit like bullets. Getting hit with an iron scourge is pretty close to guaranteed to remove whatever body part it hits. A very small siege with maybe 8 goblin lashers virtually eliminated a 30-dwarf strong militia in one of my forts before. I had like 3 dwarves left at the end, and they were permanently maimed.
On the flip side, if you can defeat a wave or two of lashers, give all of your dwarves these weapons. If they also have better armor and a shield, they will puree their opponents in no time.
Right now, until you get a large, well-trained and equipped military, your first line of defense should be traps. And after the traps fail, your second line of defense should be more traps. Then if they get past those traps, and the additional traps and magma you've set up behind that, send your military in.
I surprised the hell out of myself when I quite literally shredded an entire siege consisting of a dozen trolls, at least a dozen marksgoblins and another dozen or more macegoblins as well as a couple of elite leaders, all riding beasts, with a half dozen weapon traps with maybe 16-20 serrated metal discs among them. The first wave missed them, the second wave pathed right through them and got vaporized. Seriously. They were there, then suddenly there were no icons left. Then when the first group panicked, they ran right back through them. In the end, the only invaders left from the whole siege was a maimed Jabberer, a Rutherer, a marksgoblin riding a Giant Cave Swallow (who got shot down by my Legendary Archer) and a Troll herbalist (who finally got chased down and pulverized by a hammerdwarf).