I believe most of the things you mentioned are planned or have at least been mentioned as possible features.
* Linkable minecarts - Notch has mentioned wanting to do this.
* Fruit trees - Notch has also mentioned having more variety in the trees.
* Water mobs - We already have one, there will hopefully be more.
* Skinnable armor - Not sure if this is planned.
* A portable tent - Wouldn't that be a bed?
* Colored glass - Exists as a mod. If it doesn't make it into the final game I'm sure it would still be available as a mod.
* Domesticated animals - Notch has promised to add at least one pet.