I think invader tunneling is only going to happen when we can properly replace walls. Right now it's a 1-wall at a time and repeat ad nauseum process, because your citizens aren't smart enough not to wall eachother/themselves in if you tell them to fill the whole tunnel at once.
Perhaps invader tunnels should be a special case where they always collapse after a period of time, and the original rock is replaced when they collapse.
I like a nice orderly fortress but I'm not against the idea of siegers occasionally trying to dig into them. It could be a good challenge for a well-established and well defended fortress, and perhaps you could place iron or steel walls (or more fanciful things) at some points to make them essentially unbreachable.
Like always, magma seems the most potent solution. No goblin is digging through that. Worried about goblins with buckets ruining your fun? Destroy all the rivers and lakes on the map with magma, except for an underground channel; which you will also surround with magma. Start on a very hot map so that any water brought in from off map will evaporate before the goblins can bring it to the magma. If they somehow still manage to breach through, well, flood the world. Of course you're going to need a near infinite supply of magma, that's why you start on a volcano.
Or we could dial it back a minute -- the new military structure, and medical system, should make it much easier to keep our dwarves in fighting fit. It should be more of a pleasure to build up a strong military and use them to fight off siegers. Heck, I hope siegers get stronger, and there is that possibility. There should be more risk and more reward for sieges, eventually, and if you have a really good doctor there should be lots less tantrum spirals too.
I think off the top of my head what I'd do to counter tunneling siegers, is make my fortress a great tower with a cleared out space to all sides. Make sufficient fortifications around this tower for covering every approach, and build this tower as deep into the earth as need be. Make the bottom floor just solid steel walls, perhaps with alternating layers of bauxite. Even with every means at their disposal, and even if walls could be destroyed through realistic means (melting, hitting, crowbars), it would take years to breach from below. Attacking from the sides would take siege towers and sufficient numbers to overcome dozens of marksdwarves firing on them, and hammerdwarves at every entrance.
So, really, I'm looking forward to sieges becoming more interesting.