More nobles, definitely. But not just useless layabouts - nobles' involvement should become necessary as the scale and complexity of the fort grows, something akin to the Arsenal Dwarf of yore. For instance, the bookkeeper might need to be promoted, requirements, mandates and all as the number of goods to keep track of/population increases. The chief medical dwarf, too, might require more as the burden on his staff increases.
Much like in real life, the value of good thoughts should be diluted by how many dwarves share the thought, as well as by how frequently that thought is had. For instance you won't really be ecstatic about dining in a legendary hall if you've dined there alongside everyone else for the past year. You might, however, be upset should that situation change... This kind of happiness attenuation and adaptation mechanic might make transient good thoughts - like eating a good meal - more important to have. It will also bring strategy into increasing happiness. Laying it all on at once would no longer be a good idea as dwarves will get used to luxury. Rather, some boons like a caged exotic animal or the waterfall should be reserved for times of crisis, as their novelty will serve to increase their effectiveness.
Negative thoughts, on the other hand, should be made sharper by their uniqueness. If Urist is the only dwarf in the entire fort who has to sleep in the grass, he'll be much more upset than if everyone sleeps in the grass (though dwarves who do it often, like hunters, should get used to it). Grudges should engender (more) skewed jealousy/schadenfreude mechanics where a very good thought for a grudge causes a very bad thought for the holder, whilst a very bad thought for the grudge only causes a mild (depending on personality, of course) good thought for the holder.
In general requiring more complexity and introducing more room for fatal mistakes and cataclysmic confluences of bad luck (preferably noble-induced) as the fort grows should be a guiding principle.
For instance, to keep dwarves happy at a large population you might need to brew booze of a high quality (yes, booze quality! why hasn't anyone thought of this before?!), which might itself require a special still that consumes fuel and needs to be built over a water source.
Temperature effects could be leveraged to a greater extent (FPS beware), such a needing heating even underground in cold winter, or requiring cooling of large stockpiles of food.
Air quality and ventilation are big things that could need to be managed, especially deep underground.
Ingestion syndromes mean large-scale food poisoning with mould unless special measures are taken such as postprocessing - marination in glass jars, salting, etc. No more selling mass amounts of unpreserved food "We will not be able to eat this much food before it goes bad!"
More chronic diseases - diabetes, asthma/potter's rot, lead poisoning - that afflict dwarves based on long-term activity (or lack thereof).
Industrial accidents, more likely to affect novices - "Urist McDabblingFurnaceOp has had a terrible accident!" (his right arm's fat is gone, his right arm is oozing ...'s dwarf blood).
Reintroduce sparring injuries, nerf/dangerize (totally real word) danger rooms.
More involved enemy sieger behaviours - sieges shouldn't be supersized ambushes. Even short of enemy digging, enemies should be able to scorch the ground, dump filth/poisons where the entrances should be, etc. This combined with making underground farming/farming in general more difficult - need phosphorus source, nitrates source, etc., for sustained farming. No farming should be sustainable indefinitely without access to the surface.
I had some coherent ideas in mind but they degenerated into a list of mad ramblings, as you can see. Oh well.