That's what I like to hear! Suggestion time is my favorite time. I realize a lot of things I've suggested have been stymied by limitations of toady's work, so I'll stick to just workshops, objects, and animals, since they seem to be the most moddable.
Perhaps an alternative to cats for pest control? You could have one in addition to cats, but it could be more effective at vermin control and perhaps be less of a cute pet to give dwarves happy thoughts. It wouldn't be an upgrade, just an different choice. Faster perhaps, or flying, or both? Perhaps some dwarves could find them ugly or dislike them, to further balance them.
Of course, a *more* likeable pet, with less vermin hunting ability, could also be possible, something with universal appeal and some happy thought generation but no other utility.
Neither of those animal options would really change gameplay that much, but would offer a little variety in options for fort happiness and pest control.
Perhaps some additional subterranean animals that are tameable by dwarves? Or edit some of the creatures that already exist for that purpose? Giant worms, beetles, cave crabs, axolotl, bats? The pest control animal could fit here too I suppose. These would be largely meant to be improvements over basic animals that fill the same role. Livestock, resource production animals (wool, milk, etc), pest control, or war animals for defense. Since they are more dangerous to acquire they could be more efficient or powerful. This means that trapping, animal caretaking, and animal training would be a more important skill, and would effectively have a tech advancement option. Perhaps upgraded mechanisms (or another advancement) could be required for the traps to capture these creatures?
The early attacking but poorly equipped race possibility you mentioned as a possibility earlier would be fantastic. Since Bog trolls have moved to be a later threat, this would maintain an early (but not necessarily overwhelming) threat to work against early forts, without giving them much in return if they defeat them (no free items from weak enemies to sell or melt). Perhaps this is the plan for the moroii, but it sounds like they're meant to be an interesting addition and optional way to start the tech tree (which is a great idea, thank you!). If you have to breach the underground to see them, chances are they couldn't really be an "early threat" to work against. Ideally, this threat would be mostly able to be defeated by caravans without aid, so it would mean using wood, bone, obsidian, and leather items (or common metals) early would be useful for starting a militia and/or traps, rather than just waiting until a supply of iron or steel is available. This effectively increases the amount of metals and weapon/armor materials in the game without having to add them in the mod, since (to my experience) no one bothers making equipment out of weaker materials as a general rule. Perhaps I'm mistaken, but that has been my impression. It forces the player to scrape together more desperate means of combat early. Once they have a trained and equipped fighting force, or simply enough effective traps, this stops being a concern. The idea there is to keep the player on their toes early without beating them to the floor. Just something that would give civilian dwarves trouble, but crude weapons and armor with poor fighting skills would defeat.
Another possibility would be splitting the forge so that there are two: a common metals forge and a more powerful metals forge. One that could be used early, for making copper and bronze and the like, and one that requires a minor advancement in order to produce items of iron, steel, or better materials. Perhaps the upgraded forge could simply require more anvils and/or better quality anvils? The means by which this is made more difficult to acquire don't matter that much I suppose. It would be an additional way to force players to utilize weaker materials early and "tech up" by making more anvils or whatever they need to build the next forge. This would also make the player have to choose between outfitting their forces with as much copper / bronze / etc as possible or spending it on teching up and leaving themselves more vulnerable while they build or trade to get the parts needed. The cost to upgrade would have to be significant but not prohibitive in order to achieve that. Perhaps, instead of requiring anvils, it requires some other part made form the basic forge in the same manner that you've used for other tech advances. This would mean that the player would not be able to directly trade for the advancement, and would need to manufacture them, taking and materials to do so. The materials could perhaps be traded for, so that if you were on a map with only more powerful metals you could still use them. For instance, if you started surrounded by iron or mithril but lacked any weaker metal like copper or silver, you could trade for the weaker metals just to upgrade. This would also have the addition of making trade more vital, again encouraging players to keep their forts open for business and defended rather than walling themselves in right away.
Did the "sapper" idea pan out? Can gremlin tags be added to other race castes or creatures that could accompany a race (as trolls do on goblin sieges) to provide that additional threat of trap dismantling or lever pulling?
Anyway, there are some ideas. Hopefully there is something inspiring there.