I like a lot of the ideas here that have already been suggested, but here's a few more:

Could tech points be gained by any one working in the specialty in any area, rather than just the people doing research? If you've got a Farmer who's working in farming you don't gain anything in tech points, so you have to keep getting him to go back to the table to research instead of farming. I think that perhaps you don't gain as many tech points for doing certain things as others, but getting something for having them work in their specialty should get something.

I agree that it's difficult to get Master Builders, especially once you've got most of the buildings built. Perhaps there could be other tasks involved in building/repairing the huts that help gain points, like chopping down trees and cutting them into logs/boards, or gathering palm fronds for the roofs. You could even have part of their task be to learn to be a stone mason and build bigger stone buildings. They need something they can do when they aren't actively building an item in order to gain skill.

Mothers should definitely get more parenting skill during the time they are nursing. Setting up "family units" (not necessarily marrying a couple) might be nice, although it could definitely be optional.

I'd like to see teachers in each area of work (a Master that has been designated as a teacher, perhaps) teach their skill to the children, rather than having the children born with specific skills. This helps avoid having only researchers born (which is what has happened to me) and having to start from scratch to get farmers and builders. When the children are a certain age, say 5 or 6, the could start school, and you could designate which skill they would be learning. Teachers should also have a limit to the number of children they can teach, which would encourage you to have more Master/Teachers in each skill. So, say each Teacher can only teach a maximum of 5 children at a time. If you only have 1 Farmer/teacher, but you have 10 children designated to be taught to farm, then the oldest children get into the class first. Teachers also should gain "teaching" skill, and the amount of teaching skill a teacher has should effect how much skill the students earn. With this set up a child should be able to get far advanced before they start in the workforce on the island, although I probably wouldn't allow them to become Masters without actually doing the work.

Healers should have their own research bench at which to earn more healing skill even when someone isn't sick.

I like the idea of a nursery with someone who's mastered in parenting being in charge of the infants and having the mothers be able to do their specialty with periodic trips to the nursery area to nurse their babies. You could have things work as they currently do (mothers take care of babies for 2 years, doing nothing else) until you have a Master Parent, and then have the option of designating that Parent as the infant caretaker. Again, the number of babies that one person can care for should be limited, so that encourages you to have more Master Parents to work in the nursery. If a Nursery Specialist can care for 3 infants, it would be first come/first served, and any mothers after than who have babies would then have to care for them as normal. Of course, building the nursery gives the builders more to do, as well.

As for the livestock idea, I think it could be a good one, and give the kids more to do than just run around and gather mushrooms and collectibles. Chickens or pigs (wild boars) would be a good choice. Chickens are good because they don't require anything special, and can just run around the island in the flock, laying eggs wherever. If the farmers learn to hunt (which is an excellent idea), they could also have as a goal capturing a male and female wild boar, in order to domesticate them and raise them for food. This could involve a variety of people, because the builders would have to build and maintain a pen for the animals, the animals would have to be fed, and then they would also need to be slaughtered for food when they were the right age.

Pets are an interesting idea...they would cost more in food, but could have an effect in how happy someone was, and in return, that person could gain more skill because they are enjoying themselves more. Or, children could have pets in order to learn parenting skills before they are grown, as caring for a pet can prepare you for taking care of a child. Again, pets need to be worked into the puzzles in some way, like they find an injured bird and decide to help it heal, and it gets attached to the people, which they enjoy, and that in turn makes them want to get other birds as pets, or some such.

I think a spiritual leader is a good idea, and NOT the Golden Child. Someone who's got to Master skill in parenting/teaching/research would make sense, if teaching ends up being a skill level. They could do burials, family joining (if that's chosen as an option), and special ceremonies, like a naming ceremony where the new child's name is chosen (by us, of course!).

I also think that keeping track of family history is a good idea. With VV2 you know the parents of the children as long as they are a child, but once they are an adult you have no idea who their parents are. Keeping track of their ancestry would be nice so that they don't end up mating with their sister or some such.

Oh, another suggestion related to the nursery suggestion that I just thought of...if mothers are putting their babies in the nursery there should be an option for those mothers to have another baby after the first is a year old, rather than 2. It would help to gain population, and is also fairly realistic...I've got 2 kids spaced 13.5 months apart myself.

Oh, also, I'd really like to see a pregnancy time span, rather than them going to the mating hut and instantly having a baby. The healers could then get involved in gaining skill from helping with the birth of a baby. I'd say that there could also be the chance that a baby be still-born, but that's probably TOO realistic. I do think that during the pregnancy time the mother would still work, but maybe not work as quickly.

I also like the idea of night and day, although I'd think there would have to then be some people assigned as "watchers" to keep the camp safe from animals getting into the food supply or taking off with their livestock (if that option is implemented). Also, there should be some things that are only done during the day, and then some that are only done during the night (like getting pregnant! LOL!) to make it more interesting, because if the villagers are not doing anything for 8 VV hours at a time because it's night it would be fairly boring during that time.

Ok, that's all I've thought of so far...will probably post more ideas as they come to me!