Longer limbs is a larger stride. Yes smaller bodies have less mass to move but if their limbs can only cover half the distance per stride they'd have to make two strides in the same time as the larger body. This can become really inefficient. That's why they only get +1 Speed. This is the difference between let's say a Beagle or a Chihuahua (small bodies if a bit smaller than my intended size) and a Greyhound (lean body and fastest dog breed) and a German Shepherd (medium body). I can also use wild cats for an example lynx and caracal (small body), cheetah (lean body and fastest land animal) and cougars and leopards (medium body)
Most small animals have far larger litter sizes than bigger animals.
There are a few reasons for this but one could be said that smaller animals need larger packs to make up for the fact that they get preyed on. The other is the fact that a smaller body is quicker to develop and requires fewer resources to do so.
Only the smallest animals can have hundreds of young at a time. Spiders and Small Fish
And as you get to the larger end having more than one baby is uncommon to very rare. Elephants, Rhinos, Bears.
Small animals do not eat a "lot" more. They do in fact eat less. However they do not eat proportionally less because they have a higher metabolic rate to keep up their internal temperatures. However this game doesn't take into account size and metabolic rate and such for how much each creature eats. And with regards to Gathering the same could be said of the Bird Beak how does it offer any advantage in gathering over any other kind of mouth?
Anywho. I kept those as alternatives as they could make for more interesting and specialized creatures.
At the very least I'd like to see a small body body added because why not?
We have both Antlers and Ram horns that are no different in terms of gameplay.
We have both medium ears and round ears that both offer +3 hearing and no differences.
Then of course there are the myriad of coat options and patterns. (Which some do have effects but by large don't)