I might repost if a good agricultural thread comes up. It's not really anything that original, though, and IIRC, agriculture is lowish priority for now. I guess sieges are more on topic for the current mainly military arc.
So back on track, allowing goblins to dig, breach walls, cause cave-ins, etc., would be a decision that needs to be approached very carefully. It should generally be that goblins can do anything dwarves can (though perhaps not as well). But at the same time, it can't be so easy for gobs to dig their way in that you're better off living like a filthy aboveground humie so that you at least see the green meanies coming.
It should obviously be very easy for goblins to collapse or dig into simple dirt rooms (and maybe they could even employ trench warfare, if they know your fortress relies on projectile weapons), but they should dig stone much more slowly than dwarves.
There should be distinct pros and cons to underground vs. aboveground defenses. Underground must be slowly and laboriously dug to, but there's not a whole lot you can do to attack goblin diggers without exposing yourself. Aboveground stuff is much easier to attack, especially with catapaults, but also allows a more active defense.
In the longer term, a good, realistic terrain destruction system would be great. You'd need to build your fortress deep, with thick walls and ceilings, and plenty of supports, or a well-placed catapault stone (or a few dozen) would cave in the whole thing. Aboveground walls should eventually be potentially unstable if they're too high and/or thin.
Just better goblin AI by itself would also take the game to the next level too. It's reasonable for early scouting bands and skirmishers to blunder into your defenses, but by the first real siege, they should really be a lot more organized and intelligent, trying to breach your fortress by some tactic other than a screaming highland charge down the corridor of death.
Use of ladders, grappling hooks, and other climbing tools could certainly make some fortresses harder to defend.
If disease is also implemented in this next version, the goblins could even use biological warfare by flinging corpses and poo!
A realistic need for air circulation would also increase difficulty enormously, as goblins could try to find your air vents and try to smoke you out with fire, stink you out with miasmic filth, etc. Air circulation could potentially be way too much for newbies, though, depending on how it's done. I'd just do a simple rule, like X tiles must be open to the outside for every Y tiles of volume in your fortress. It would certainly eliminate the old "just one entrance" design philosophy. Combined with terrain destruction and climbing, a large fortress could be very hard to defend.
Things which make sieges really hard, though, should be be saved for a version where diplomacy is better developed. Like before, I'd suggest a low-maintenance and high-maintenance approach. The low-maintenance one would be allying with someone and getting them to protect you in exchange for goods, services, whatever. Costs you money (possibly quite a lot), but you don't have to worry too much about sieges, as your faithful humie pals march off to their deaths under the scorching light of the evil sky-orb. But handling a big, late-game gobbo siege all on your own should be extremely difficult (and extremely satisfying to beat back). And of course, it should also be possible to negotiate peace (however temporary) with the gobs.