The world of the future has no disease or microbes. But, the Time-Traveler must have brought microbes from the past and the Eloi and Morlocks were pawing him all the time, so... well, remember what happened to the Martians?
For all we know the reason the Eloi and the Morlocks have no disease is the result of genetic tinkering or immunization which would make them immune to all diseases, past and future. Smallpox may be almost wiped out, but we still immunize against it.
On the other hand, the scene in the library suggests that natural decay has been greatly slowed through the extinction of most bacteria and fungi that would normally cause decay.
While the strange, flopping creature seen in the far future near the end of the book seems at first to just be a part of the scenes lonely, cold vision of a dying world, context increases the level of horror. HG Wells, along with many other writers of the time, was familiar with the Victorian idea of human evolution eventually favoring intelligence over strength to the extent that mankind would become nothing but a brain with frail, tentacle-like appendages. In this case, however, the strange, probably marine creature is a stomach with frail, tentacle-like appendages. The implication seems to be that it is the last remnant of humanity in a world where even the monstrous crabs are freezing to death.
The Eloi display numerous expected signs of Artificial Selection on the part of the Morlocks:
the reduced intelligence they display could have any of a number of intended benefits: 1)To make them more complacent, 2)to make the brain take less sustenance away from the rest of the body (in modern humans, the brain uses 20% of the body's oxygen supply despite comprising a mere 2% of it's mass), or even 3) to make it less of a moral conundrum to eat them. Furthermore, they also display signs of Arrested Development relative to modern humans, which is extremely common in real life domesticated animals.note It results from our ancestors selectively breeding the animals that tried to attack us less often, which unknown to us at the time was because the animals in fact had arrested development. Admittedly the Eloi would be more convenient still in these aspects if they were outright as dumb as sheep, but it's possible that the Morlocks were trying to get them there and the Time Traveler simply arrived at a point before they'd quite reached the finish line, so to speak.
What's more, they also display signs of Neotenynote The word for when evolution occurs by retaining infantile or juvenile physical traits into adulthood, such as if a hypothetical species of frog were to evolve that remained tadpoles their entire lives and ditched the actual frog stage, which might be reasonably expected if the Morlocks were trying to breed them to mature faster (modern humans actually mature ungodly slow for creatures of our size; modern cows are able to start popping out more cows by their first birthday).
Admittedly this does raise the issue of why the Eloi still have the muscle mass of a modern human child, but it's possible that the Morlocks decided that packing on the protein before they've got the Eloi perfectly dumb and docile would be a verybadidea.
