If they're features not everyone will use they probably won't be coded into the core. When a battle system does exist, I imagine most of the latter half of the list will exist.
(An item function that raises a pet's level already exists.) -- (The item functions aren't very intuitively named, but they exist in
functions/functions_items.php, so I know that giving an item the function 'level1' will increase a pet's level by whatever you set it to while creating the item.)
I agree that both items and pets should come with a rarity field (what that means for pets isn't so obvious).
I added a rarity field for my items, and Tahbikat created a mod for
pet rarities. I also feel we should get shops that stock items, rather than simply always being there... and then rarity would make sense in a stocking-sense.
And actually making custom item functions isn't so bad, see this
Gender Change Potion. If users have custom needs for that sort of thing it's easy to imitate code for existing items. It's pretty easy to modify even custom attributes given to pets... like say from the
Stat/Skill mod (if you want to use that,
see this post, because I did a write up on the missing images and changes needed for v1.3.4).
I don't see stuff like that ever being built into the core, but, what we DO need is solid documentation on how to continue to do things like that in newer versions.