Apart from the bar sometimes being crowded I don't recognize much from when I was on Gem just before Christmas.
Cookies - Available every day at around 3 pm in The Great Outdoors. Should be listed as "snacks" in the dailies. OP, did you ask anyone if there were cookies somewhere? Or did you just roam around hoping to run into some cookies?
Once a day room cleaning - Old "news"! Unless you need assistance with a third bed or something I honestly don't get why anyone would need any turn down service anyway! If you do need assistance I guess you can request it.
Towel animals - seriously? Nice, but surely the steward has better things to do! As has been mentioned, you can request them. And of course you should tip accordingly (whatever that is).
As for general cleanliness there was no such issues during my cruise.
I thought Gem was an amazing ship! Yes, showing her age a little, but in general very nice!