Well, this hasn't been tested quite as much as I like, but it's been a while since I last updated, and most of the bugs have been fixed (they were mainly caused by Piranha Plants, so they've been simplified, for now).
I'm calling this one the Alchemy Update. A word of warning: this update increases the difficulty of the game somewhat. Even if you hurry, it'll probably be about a year or two before you're able to start producing the high-level buildings and reactions. But it's also more rewarding when you do. The alchemy is also quite a bit more complicated than before, so this update comes packaged with a guide (which is not as well-organized as I'd like, but there's time for improvement).
The main change to Toads is that they can no longer produce warp pipes from any pipe sections - instead, they'll have to convert pipe sections into warp pipe sections by using... their own concentrated vim (or 'azoth'). What? Well, warp pipes are green. Toad vim is green. The Shroobs were extracting vim to power their spaceships. Think about it... Anyway, you extract and concentrate vim in a still. Be warned that this will actually drain some blood from the Toad performing the reaction... it won't kill them immediately, but keep an eye on your self-brewer, and if you see them start to flash (indicating low blood levels) give them a rest or find a replacement.
As for Koopas... they now have two new castes - Burly Koopas and Magikoopas - and a caste-based noble system (so for instance, the civ's Oracle will always be a Magikoopa). The mayor can set up Burly Koopas as Brutes who can run a more well-organized military even without a proper land-owner, although with the added difficulty of keeping a bunch of whiny (and quite dangerous when berserk) nobles satisfied. Natural births of these two castes are quite rare, but you can transform regular Koopas into them using potions.
Creating the potions is fairly complicated - you'll need a fire-charged gem and 10 jars of azoth. Charging a gem requires magma (or you can now make a non-magma charge point if you want to burn down an entire forest to create one gem - not recommended but hey, it's an option) and azoth requires 10 shining coins dissolved into alchohol. A bit of a steep price...but you can use either 1 unit of azoth or 10% of a gem's charge to burn away an obsidian boulder (or if you're missing obsidian, turn a regular boulder into an obsidian boulder), creating a fire stone (for lava pit creation) and a 10% chance of making a carmot gem (aka the Philosopher's Stone). Which can then let you convert any natural metal first to silver, then to gold, and finally to shining gold coins. So getting started can take a long time, to be sure, but once you get the ball rolling you'll be able to start producing all the potions and shining gold coins you need.
As for Shyguys... well, they're now officially 'hard mode'. Enemies from every direction... and not even a single squad to fight them. At least at first. Hope you like cage traps and siege weapons! Once they've built up a sufficient population, they'll be able to start assigning nobles. But sticking with them isn't without reward... they can use a 'Coloring Workshop' to paint wood and stone, boosting their value (before carving them - don't ask how that works, they're Shyguys), fast-grow plants (even those that can normally only grow in other biomes) and cross-breed powerups in a Gardener's Workshop, and once you get enough coins to play the slots for a magic potion (which must be grown from a seed) you'll be able to open up a Subspace Portal and produce Subcon Crystals, which will allow you to produce temporary items or permanent blocks from a Dream Bed or a Toy Box, respectively. Oh, yeah - multicolored blocks are back, and now come in six eye-hurting colors (and you can choose which ones to make if you're OCD like that). A Magic Vase will give you access to infinite white sand (for use in the Coloring Workshop) and will sometimes produce keys to be used with a Subspace Portal for better rewards. But you'd better keep it well guarded...
By the way, if you need coins or other items, flying ? blocks now work properly. When they fly in, wait until they stop moving, and if they stop out of reach in midair, quickly construct a stairway up and send a soldier to punch them. Hey, you ain't Jumpman. They can be opened at a Craftman's Workshop.
One of the reasons for all of this is to increase the benefit of cross-species reclaims. What does this mean? Well, since all groups use more-or-less the same materials in their reactions, there's added benefit to reclaiming a fort abandoned by another species rather than starting a new one. (Koopas reclaiming a well-established Toad fort, for instance, can make good use of the Power Stars and piles of coins they find there, and Shyguys can dissolve a carmot stone to produce a free Magic Potion right from the start). Also, some species can utilize workshops that can only be created by another species - for example, only Toads can create a Toad House or Warp Pipes, and only Koopas can create a Golden Chest, but anyone can use them once they're made. There are even some 'secret reactions' that can only be used by a species with access to a workshop built by another species. For instance, Toads with access to an Alchemist's Workshop can 'meddle with dark forces best left untouched' (animate all corpses) and Shyguys/Koopas can desecrate a Star Beacon altar (causes one or more of several fun effects...usually bad ones, but hey, you might luck out and get a vampire, or a pet Artichoker).
I've also included a copy of the DF executable, which has a couple of language file changes. Nothing too major, just some minor flavor stuff, like getting Bub-ulbs to stop referring to themselves as elves and having more Mushroom Kingdom-appropriate month names.