From God's perspective it could be perfect - even if no individual organism thinks so.
So the question is, what gives us the right to decide what's perfect and what isn't? Our perception of perfection is obviously subjective, since it relates to what we think would be best for us. But true perfection isn't subjective. True perfection is the state of being complete and whole with no part missing, finished, and not able to be improved upon.
In science something is called 'perfect' when it follows some physical law or mathematical equation perfectly - eg. a perfect crystal, a perfect sphere. Our laws of physics are only approximations of the real laws governing the Universe, but imagine if we had a law of everything, where every particle and wave in the Universe was following that law perfectly. By following that law perfectly, the Universe itself is perfect.
An organism may complain that the Universe can't be perfect because its life isn't. But it is made of subatomic particles and waves that are behaving perfectly. Any deviation from that would be less than perfect, like 2+2 adding up to 5 instead of 4. So the organism's perception of imperfection is just the result of the Universe working perfectly.