Sieges don't show up until you have 80 dwarves in the first place, and so you should get yourself prepared for that before it happens by creating a device (as simple as a raising drawbridge linked to an interior lever that blocks your only exit) to lock the fortress down in case of emergency. Goblins get bored and leave eventually, and you can expedite this by shooting them with crossbow bolts, caging them en masse as described above, weapon traps... If built properly, ballistae can be effective, but you need to be pretty dedicated to them and there's always the risk of your civvie operators pissing their pants and abandoning their post.
As far as designing your fort and not liking it, it's often more Fun to just suck it up and deal with it. You can fill imperfections with constructed walls, and then later, when you have MMMMMMMMMMAGMA, you can use careful obsidian casting to fill the walls back in and then dig them back out again later.
I've also recently experienced the same situation you're in and a similar epiphany relating to what Verdant described. I joined up an amazing pseudo-succession game where instead of building a fortress, the players are building the RAWs from scratch. I took the first player turn, embarking with a squad of halflings (who are water-dependent and not booze dependent) on a river that froze in winter. It started out frozen, so I knew it would freeze in winter and that I'd die if I didn't do something about it. But I got distracted doing what I'd always done, setting up industries, and winter came and the river froze and everyone starved to death before I could fix it. It was a learning experience, and what I learned was that Losing Is Fun. I'm no longer as paranoid about my forts being super efficient and perfect. If I obsess over these things neurotically, I'm never going to get past the starting couple years, and it turns out that letting some of this stuff go isn't necessarily lethal. And if everything goes to hell in a handbasket? Makes a better story that way.