Clue explanations and solved grid:
The thing Cryptic Cat hates most of all is
It's not actually necessary to associate letters to digits to get the final answer - it can still be done, though. Here's one of the many possible logical paths you can take:
My prefix is my abbreviation.
My infix is.
My suffix is seeing something.
Together, I need someone like you.
My prefix is a place.
My infix is eating something.
My suffix is suspicious by its presence.
Together, you cannot let the one like me be nothing.
I think you might be
Me, I cause pain.
My first anagram is naturally beautiful.
My second anagram is synonymous with rocks.
My third anagram is fancy food.
My homophone is what two brothers wanted humanity to do.
My homophone’s anagram can direct and achieve motion.
My anagram’s homophone, is how you use the previous clue(plural).
They all reflect the concept of time.
A lightbulb is a symbol of the humanity's progress through time; it's an artificial image of sun, the one thing that guides us through the day.
A forest is a unit of time, 17 seconds or so.
The hole in the tree is a circle, quite like a clock. That wood, when put vertically, has a shadow that tells us the time.