Everything that has been said so far sounds good. As you already know, dwarves have a lot of bloat because they were designed first, before the idea of having multiple specialized races even existed, and many of their functions (I'm specifically referring to things that involve transformations) exist as they are because they were designed before better, DFHack methods for those systems existed. Your planned changes sound good, although I'm a bit iffy on the drilling rig... I guess it depends on how 'steampunky' you want your dwarves to be.
Concerning gnomes, I would like to port them over. The machine code has to be redone though, as it's kind of buggy right now. Rubble includes the basic machina system, presumably with a great deal of bugfixes. I don't want to leave them as they are in Rubble (no factory related traps/accidents? Laaaame) but I might use that as a starting point, once I figure out how it works.
Beyond that, I'd say wait a bit before deciding whether or not they should remain active. The new DF has a lot more complexity when it comes to determining who sieges you, so it might be possible to prevent gnome sieges by messing with their personalities and civ values.
One other change that hasn't been brought up too much is the wild animals. They were all kind of ported in from various different source mods, without much in the way of universal cohesion or theme. Supernatural creatures seem too common, for instance, and petvalue is all over the place. Also, the NATURAL tag is kind of thrown around without much forethought, admittedly because it doesn't matter much for most races, but it does determine AT_PEACE_WITH_WILDLIFE, so it would be nice to have that aspect be a little more intuitive. (Giant spiders: friendly. Great Cow: not friendly). This will require a major overhaul, but I guess it could be done a little bit at a time. There should probably be an overall plan first, though.