With old science fiction it's always interesting to look at how it stacks up to today's scientific knowledge. And The Time Machine holds up pretty well.

Biologically there's an engineered world gone feral, and the evolution of the Eloi and Morlocks is very much in line with the selection pressures (or in the case of the Eloi, the lack of selection pressure) that they've lived under. The Eloi are neotenous, never emotionally developing much past childhood, much like housecats when compared to their wild cousins. And it's not treated as an endpoint but simply a later stage -- one which spirals down to extinction because ultimately, neither the Eloi nor the Morlocks are resilient enough to survive in the long run. In the distant future, the time traveler sees a post-human world in which insects and other wildlife return, the garden landscape returned to the wild.

It was written only a few decades after On The Origin of Species, and Darwin's theory of evolution has just kept collecting more and more evidence since then, with a lot more incremental refinements than major changes.

Astronomically, the time traveller remarks on the constellations being completely changed, but the Milky Way still being the same. Motion of stars has been known for a long time, but we didn't know what galaxies actually are -- or that there are so many more of them than just our own -- until several decades later. But the sun's path within the galaxy is going to keep it within the same band and around the same general distance from the center. The hazy view along a disc of distant stars is still going to be a hazy view along a disc of distant stars. It's not going to look exactly like it does today, but it'll be in roughly the same part of the sky and look similar enough to be familiar. And in the far, far distant future, it certainly seems possible that Earth could become tidally locked with the sun (which would definitely alter weather, wind and waves considerably!), and we do know the sun is the type of star that will become a red giant. The only thing that seems off in that scene is that there's still (barely) enough oxygen for him to breathe, and that one of the inner planets has moved outward toward Earth instead of just being swallowed up by the sun as it expands.

Geology is a bit sketchier. He stays in the location of London, and can still recognize the landscape even with all the buildings gone, but it seems like there ought to be more of a difference after almost a million years. Even without considering plate tectonics (not yet discovered) and continental drift, just ordinary erosion ought to have changed something in a river valley. That said, it's a good thematic choice that strengthens the link between the future world and the then-modern society being critiqued.