Terraforming and ecology... People do not like having their livelihood threatened, or food taken from their children's mouths. People do not like their profits being reduced. People do not like putting in days and days of work, and seeing some or all of that work damaged or destroyed. Farmers are people, just like all the rest of us.
Since the dawn of agriculture, farmers all over the world have invested significant effort into driving off or killing creatures which harm their crops and their livestock. That's everything from scarecrows, to aircraft spraying fields with pesticides, to putting a bounty on the head of wolves, to gassing badgers which may be carrying bovine TB, to genetically engineering plants which are resistant to plant viruses. If you terraform a world and you take things like aphids, locusts, wolves, foxes, the cotton boll weevil, the Colorado potato beetle, the tobacco mosaic virus and other such things, then the farmers on your planet will - at the very best - be writing strongly worded letters to the Times. At worst they'll turn up at your house with torches and pitchforks!
Building an ecosystem with all the wild creatures which conservationists like but which farmers consider to be pests and vermin (e.g. golden eagles, foxes) is on economic terms, bonkers. There are whole industries built on defeating the depredations of crop pests and eliminating vermin from our homes. Why soend this money when you don't have to?
Building an ecosystem with all the wild creatures which transmit diseases to humans and domestic animals (e.g. malaria, foot and mouth disease, TB) is probably socially disastrous. Mrs Miggins can emigrate to Planet A, where her kids have a chance of catching some hideous disease or parasitic infection, or she can emigrate to Planet B, where those diseases were not incorporated into the ecosystem. No contest. (Unless she is from some society which believes such things to be character building or that human suffering is part of God's plan). It is kind of like designing a new city and deliberately including muggers, road accident blackspots and poor sanitation.
If you miss out all the 'inconvenient' animals, plants (weeds) and diseases, you have a very impoverished ecosystem. We don't really know those will function, because there has never been one on Earth. We might be able to design a stable one, we might not. There is a certain amount of flexibility and adaptability even in existing systems, but humans may have to step in to keep everything on track.
For example: consider the differences between grasslands in the Americas and Africa. In the Americas (before the Pampas and Great Plains became farmland), the main cause of death of the big herbivores like buffalo and deer was being killed by large to medium carnivores, such as pumas, wolves, coyotes. Some of the herbivores also died of famine, drought or disease, but predators are the main thing that keeps their numbers stable. Ecologists spend many a happy hour modelling predator and prey population cycles.
In contrast, in Africa the main killer of big wildlife is famine and disease. Sure there are lions, leopards and cheetahs, but they are a minor factor. Africa has, as a result, a huge 'scavenger guild' - animals which make their living from eating the deceased. There are scavengers in the Americas, but Africa has them in droves. Vulture species which specialise in eating particular bits of the carcass. Specialised bone eaters like the various hyenas or the lammergeier. Basically a whole bunch of animals which either only
eat carrion, or mostly eat carrion.
So you can have a system which relies less on big carnivores to 'recycle' the dead herbivores. Next step is the get rid of the big carnivores altogether. I mean, you want the cause of death of your goats and cattle to be a slaughterhouse, not a leopard or a wolf, don't you? And they won't be dying of disease because you didn't bring rinderpest or tick fever with you. Famine/drought you cope with with technology, cull the herd and freeze the meat if you can't cope, and hope your insurance company pays up so you can get a new bunch of goat and cow embryos grown up for next year.
Now if there aren't
any predators, parasites and diseases, you can perhaps do all sorts of imaginative things with your domestic animals. Fast-growing breeds with short legs, because they don't have to flee from predators (lots of modern western pig and sheep breeds are like this already, as are the wild Svalbard reindeer). Cattle as big as Indricotherium (Baluchitherium)? Genetically engineer mammoths to graze your steppes, and everyone can have a mammoth-wool coat and scarf?