I love this idea!
Even in the real world, you never know what you might run into while tunneling. And in a fantasy world, it should be even more interesting!
And I love the idea of huge 3x3 trees. In some fantasy stories, people and elves do live in such trees. In at least one story I know of, an entire town is located in a single HUGE tree, that covers several acres.
And plants that fight back, or are simply annoying, like the miasma spitting fungi would be great!
Ok, sure, some of these things would mess up the plans for a neat and orderly fortress, but things like that happen in the real world all the time. And I think it would be interesting and fun trying to either build around such things, or to find some way to incorporate them into the fortress. Like in the old version, I used to try to build dining rooms next to waterfalls, to give the dwarves a boost from seeing the falls.
And I would love to see ents come to seek revenge on anyone destroying one of the great ancient trees. On a treed map, they could even be invisible unless someone is standing right next to them. And hiding inside wont help much, because they could tear into the rock itself, to come in after you. Or they could send roots down into your halls, to strangle dwarves as they walk by.
I love this game, but sometimes things right now are just too predictable. In the last few days I ran into a few surprises (Like an ARMY of chasm creatures living out in the open in a mountain valley, and that went to war against a kobold cave on the same map. THAT was fun!). But most of the time things are very predictable, and sometimes even boring. Digging into a Pit, at ground level (Under a big mountain peak.), and watching the year-old fort being torn up by tentacle demons was fun, but a bit more lethal than I would generally like to see. But hitting some less lethal caverns and such would be a lot more fun.