I have to agree that it would be easier once we see what's in VV3. I can think of a number of things, but I have intentionally not read any of the threads about developing VV3 so I wouldn't accidentally run across a spoiler (you know how my mind links things together, right or wrong).
I know that I would like a few of things right off:
1. The ability to put notes in the villager's files. I'm currently using their name space for notes.
2. I'd like to have the ability to click on a villager and immediately have some idea of their skill levels other than just info on the skill they're working on right then. Since Trainee and Adept are very generalized, just seeing that a villager is Adept does not show if that villager is at the bottom of that ranking or the top. So I now add "new" or "bars 1" or "bars 2" etc. in the name field to tell me approximately where they are in their current skill. But I'd also like to be able to see what other skills they have mastered (or not).
3. I would like a listing of the villagers, similar to a spread sheet where each villager is listed in a row with their skill levels represented as a percentage of completion. So the rows would be the villager's name. The columns would be Farming, Building, Research, etc. Within each cell block would be the percentage of how they're doing. This would make it very easy to keep track of the villagers and to spot the ones lagging behind.
4. I'd like to be able to designate special outfits for special meanings in which, once I designate it, it can no longer be automatically used for children. OR I'd like to be able to change children's outfits. I use the clothing as another way to mark my villagers for recognition at a glance, but when a child is born wearing one of those outfits, I have to be sure to catch it when s/he turns 14 or I might not catch it until a VV year or two later.
5. I'd LOVE to be able to not only change their clothing, but to change the colors of each outfit and add accessories (shark tooth necklace!). Maybe these accessories can also be tied into skill levels earned. I'd rather not have to pay to change their clothes. With VV2, it's either you can or you can't do it. At first, you have to use all your points for increased skills, but after that, you build up so many points it no longer matters. Just do away with the points for clothes. But make certain clothes and accessories available only once a villager has reached certain milestones and/or skills.
6. I would hope that wherever the children gather for their lessons when a master parent is teaching, it is not smack dab in the middle of the fishers' trail! I'm sure being trampled on by the the fishing villagers is hard on the students with ADHD.

7. I want MORE EVENTS. It's a little boring to get only one event every few days.
8. I'd like some mischievous kids and ways to discipline them (pulling weeds in the fields, for example). Just something to add some spice to the game.
9, I'd like to go with you all the next time you're island hopping for ideas for the game (yeah, sure...

).
That's what I can think of at the moment, but I betcha some of this is already going to be seen in VV3. I think the more details of any kind, such as doctor's instruments, clothing accessories, wild animals roaming around just adds to the game. And the more the villagers can interact with any of these things, the more fun it is.