Question: People often say, including those with extensive knowledge in biology, that a certain species of animal will evolve in one way or another:

1. From changing environments.
2. Mutations.
3. Possibly even genetic engineering from human animals.

My question lies in the fact that, aside from the latter option, why haven't any differences in animals'(except humans) markup, morphology, intelligence, DNA, behavior, or any habits changed over thousands or (possibly millions) of years?

A cockroach has had the same behavior it has today [more than 10 million years ago](http://en.wikipedia.org/wiki/Cretaceous), and there have been no advancements in the species in the slightest bit. 

It makes you question evolution, because why don't other animals (like cockroaches) have any changes over 10+ million years, yet humans, like me and you somewhat, have, in a relative period of time similar to the linked geological period above, evolved from spear tossing hominids into someone brilliant enough to even ponder this question.

If modern humans are the result of mutations in genes, why has no one species over the course of hundreds of millions of years been fit enough, or advanced mentally as we have, or even in any slightest bit?

Answer: 
> 
> aside from the latter option, why haven't any differences in
>  animals'(except humans) markup, morphology, intelligence, DNA,
>  behavior, or any habits changed over thousands or (possibly millions)
>  of years?
> 
> 
> 

What evidence is leading you to that conclusion? For horses, example. (From the talkorigins article):

> 
> The first equid was Hyracotherium, a small forest animal of the early Eocene. This little animal (10-20" at the shoulder) looked nothing at all like a horse. It had a "doggish" look with an arched back, short neck, short snout, short legs, and long tail. It browsed on fruit and fairly soft foliage, and probably scampered from thicket to thicket like a modern muntjac deer, only stupider, slower, and not as agile. This famous little equid was once known by the lovely name "Eohippus", meaning "dawn horse". Some Hyracotherium traits to notice:Legs were flexible and rotatable with all major bones present and
>  unfused. 4 toes on each front foot, 3 on hind feet. Vestiges of 1st (&
>  2nd, behind) toes still present. Hyracotherium walked on pads; its
>  feet were like a dog's padded feet, except with small "hoofies" on
>  each toe instead of claws. Small brain with especially small frontal
>  lobes. Low-crowned teeth with 3 incisors, 1 canine, 4 distinct
>  premolars and 3 "grinding" molars in each side of each jaw (this is
>  the "primitive mammalian formula" of teeth). The cusps of the molars
>  were slightly connected in low crests. Typical teeth of an omnivorous
>  browser.
> 
> 
> 

So from that, you conclude that the DNA, morphology, and intelligence of horses hasn't changed at all in 50 million years?
In response to this part:

> 
> If modern humans are the result of mutations in genes, how come no one species over the course of hundreds of millions of years has been fit enough, or advanced mentally like we have, or even in any slightest bit?
> 
> 
> 

All animals *are* the result of evolution, which includes mutations.

Now, what you should understand is that evolutionary changes have to be selected for, but also must be immediately useful to the organism if they cost more. 

There is a long term tendency in our lineage towards increased brain sizes. Animals -> Mammals -> Primates -> Humans. This long term development need not have happened in the first place. In the Jurassic Period, the most successful group of animals were dinosaurs, who in general had small brains.

In addition, our brains require far more calories than the brain of, say, a chimpanzee. Even if you have a lineage that, over the generations, has a tendency towards larger brain sizes, it would also need to be able to hunt or forage more in compensation for the increased caloric needs. If it were not able to do so, a larger brain would actually be a profoundly negative characteristic, a useless drain of energy.

In addition, the benefits of increased intelligence are highly circumstantial. Consider if you gave a cheetah all the brain power of a human. It might then understand that if it dug a hole and placed fake grass over it, it could catch an antelope for less effort than having to stalk and chase it. Less effort means less calories expended and ultimately most of an organism's fitness has to do with how much energy it expends in trying to procure energy (calories).

But lacking opposable thumbs and hands with digits, it would be unlikely to accomplish such a thing. Also, such tasks are more efficient when done by a group, but many animals do not coordinate group-wise as extensively as humans do. So what we have is at least 3 but probably many more things which all have to come together in the same species for them to rise to the top of the food chain like we did:

* Dextrous limbs (i.e. opposable thumbs and seperated digits)
* Brains tripled in size (relative to other species of ape)
* Behavior of extensive group coordination (tribes)

As you can imagine, a species evolving our intelligence and using it to dominate the local ecosystem as extensively as we do is therefore a rarity.