1. Not sure about the letter system not one of my favorite parts and I am still building my house so have not gotten down to letter writing yet.
2. Yes you can store more like Brain said but you will have the same items in every storage item you own...in other words if you have a chest of drawers and buy another to store more you can not the same items are in every storage unit you own so you max out at 90 items.
3. There are no diaries that I have seen
4. No island
5. No train
6. No Bob
7.Mario Clothes how to's are in the Guide
8. yes they do still move and they also move when you don't
9. ???I am totally not sure what you mean
Some things that are different:
You do not have your own house you share a house with 3 other characters, more fish, more bugs and a bigger house.
Nooks has a beauty place where you can change you look.
You can now wear hats, sunglasses only one pair of shoes still I think.
There is a coffee shop at the Museum.
An Observatory where you can make and name your own constellations.
As with the last game you need the guide.
Remember this is not a gmaecube game but a DS game so some of the Great things about AC Cube are not included and I miss them. I hope they decide to do an updated AC Cube soon!
I also wish we could interact with the DS and the Cube versions.
Mal