Everything is part of God's plan! (Or Nature, if you are not religious.)

Mosquitos that carry loads of parasites and viruses? A major food source in places where they thrive. Not for us directly, but we do eat things that eat mosquitos.

Tsetse flies? They have protected a lot of the wild animals in central Africa by making their areas uninhabitable by humans!

A lot of our feelings about animal A being preferable to animal B, are pretty subjective. One is cute and furry. One has lethal venom. But rabbits are cute and furry, and introducing them to Australia was a disaster. Fighting extinction is silly. Extinction is a natural event, like forest fires. Put them all out, and you just make the situation much worse. Maybe a reasonable objective value is diversity: A lot of different species is better than monoculture, at least in terms of stability. But specific animal populations? They usually fluctuate in a predator/prey cycle. Evolution is amazingly talented in this aspect. Cicadas have 13 and 17 year cycles because their predators have cycles with shorter periodicity. Their prime number cycles do not line up with their predator's cycles, so they have longer term survival. Some researchers modeled what would happen if they didn't follow those cycles, and all simulations ended in extinction.

One of my favorite examples is the Gnatcatcher: On the endangered list in the US, and all sorts of legal decisions have been made to "protect this endangered species". Except they are genetically identical to the Mexican Gnatcatcher, and interbreed freely across the border. They are NOT endangered in the US at all. Some years their range moves North to include parts of California. Some years it doesn't. It's really a climate thing, like El Nino. They can't read the Welcome to The USA signs!

We're flying electric helicopters on Mars yet you can't turn on your clothes dryer in Texas. That's because scientists are in charge of Mars, and Republicans are in charge of Texas.