The final scene is an Ironic Echo of the departure from Nova Prime, where a crippled Ranger asks to be helped to stand up so he can salute. In the first scene, Cypher proudly returns the salute, but in the final scene, he gratefully accepts a hug from his son. Despite Kitai having pulled off the monumental achievement of Ghosting and killing an Ursa single-handedly. The brilliance is that though Ghosting led Cypher into a highly decorated military career, the inherent inhumanity of fearlessness severely fucked up his civilian life - he lost the ability to properly emote, even to his wife and son. So when Kitai rejects the salute and instead hugs his father and says he'd prefer to work as a civilian with his mother, he's asking if he has to follow in his father's footsteps as a Ghost. Cypher accepting the hug means that he agrees that the cost is too great, showing that he will retire and join his family.
According to the backstory, less than 1% of humanity managed to leave Earth before civilization collapsed. It's probably safe to assume that with a whole lot of sick, starving and/or freezing humans around without the protection of civilization, wildlife (evolving more rapidly than normal courtesy of the destroyed ozone layer/increased UV radiation) probably had several centuries' worth of humans to prey on.
Evolution does not work like that. Increased UV radiation exposure kills things via mutations and DNA damage - it doesn't make them hyperevolve. They could've easily come up with another reason for Earth having such creatures (or simply set it on another planet).
Why couldn't the probes get the beacon? They could clearly move a lot faster than Kitai. Even considering that they lacked the ability to manipulate the environment, why wouldn't they have some rudimentary capabilities for that, when the humans clearly have the technological capacity for it?
For that matter, why aren't the probes themselves equipped to serve as beacons? They clearly have transmission capabilities if they're sending data back to Cypher, and the beacon isn't all that big, so it's not like it'd drastically weigh them down to include one.
Why climb up a volcano in order to improve the signal, when the enormous ash cloud crowning it is the most likely reason the signal is so poor in the first place? For that matter, why does the beacon need reception at all? It's a beacon, is supposed to generate a signal. Considering how strong the signal appears to be at the end, it seems unlikely the ash cloud would stop much of it.
The fact that humans can become invisible to the Ursa when conquering fear, thus fooling the Ursa's ability to sense fear, would suggest that it can't detect humans with any other senses. Why would aliens genetically engineer a monster that kills humans, and then only give it one sense to detect them with? Better yet, why would they not give it eyes in the first place? Pheromone sniffing is a handy trait indeed but why not eyes also? It's like giving the Predator only its tech supported infrared vision but not its regular non-tech supported vision. Also, if the Ursa could only see humans if they emitted fear, how was it able to locate the corpses of the dead crewmembers and hang them up?
Possibly the aliens captured a few humans on the sly, and equipped the Ursa to detect how their captives smelled. Said captives were scared half to death at the time, and that emotion-specific aroma happened to be what the Ursa's senses cued in on during their training, not the normal scent of someone who's not afraid.
These aliens were advanced enough to genetically engineer a creature to detect specific human pheromone signatures, but didn't realise that a human wearing any kind of enclosed bodysuit would be completely undetectable to such a creature?
Whose to say that the Ursa weren't created from an existing creature that was based on pheromones? There are plenty of creatures that are practically blind and have no use for eyes but rely stronger on pheromones. As for your point about the corpses, I think that the many lights that were on the map near the start were survivors who didn't die in the crash. Since two lights were right next to each other (Kitai and his father), there were most likely survivors who were hunted down by the Ursa then used to instill fear in any who saw the corpses.
More complex organisms without the ability to sense light live almost exclusively in places where light is scarce (deep sea, caverns etc.) on Earth, from this we can conclude that sight must be a huge evolutionary advantage. Also creatures with just one type of sense are exceedingly rare and even yet: Sensing pheromones is normally a subset of smell, but somehow these creatures are so overspecialized in it that just stopping "one" pheromone production (as opposed to all the other scents we also produce) renders people invisible to them? Why weren't these creatures hunted down already? Or better yet how can they survive without bumping into things? (Most stuff (trees, rocks etc.) doesn't produce fear pheromones. Theoretically they could mark / memorize their territory but this wouldn't work outside of it, not to mention how much work it would involve.) How do they mate? They would need to smell other things and/or have more senses to navigate, but those would also make Ghosting less effective (if not break it completely).
There are no organisms known to nature that overspecialise in senses to the complete (not just diminished - a complete lack of) exclusion of sight. Even creatures that hunt via echolocation can SEE. It's a huge plot hole.
In fairness, there's plenty of 'huge evolutionary advantages' that other animals have that humans don't, but we work OK without them; what's to say that the alien beings humanity are at war with didn't originate from an environment that lacked light or simply never evolved sight because of the strength of other senses? As for the Ursa, it might just have a super advanced sense of smell and other senses, but uses the smell of fear pheromones to track food sources; it can identify everything else in its environment easily, but it associates fear with food and so doesn't care for anything that doesn't smell of fear. Of course, by that logic it would probably identify other smells too, but...
Turn it around: maybe the Ursa originally did have other senses, but the aliens who keep dumping them on Nova Prime had to strip them of all the others because the creatures were so damned vicious that they'd attack anything at all, up to and including one another or their alien creators. Rather than tone down their attack-dogs' indiscriminate aggression, they eliminated their ability to sense anything but their designated targets. For the moment, that's humans.
Humans can simply put on an environment suit, and they could be three feet from such a creature and not be detected. How does the creature avoid obstacles? If it uses some other sense to avoid (for example) falling off a cliff, that sense could also be used to detect the human-shaped object next to it.
Although that one did very nearly walk off a cliff when Kitai was clinging to its back.
Why would all the animals on Earth evolve to become to the perfect predators for humans when humans left earth? Did that happen before they left? Otherwise, that would be like a deep sea fish adapting to survive elephants. Even leaving aside the hyperbole or ignorance of the statement by Cypher, the flora and fauna of Earth is clearly ridiculously dangerous to humans.
The above Fridge Horror proposes an answer for how they'd 'evolve to kill humans', given than only some humans managed to escape while the remaining majority were picked off by the predators. Its still stupid, but that's probably the best explanation.
Still doesn't explain how it happened in a mere thousand years.
Nor does it get around the minor detail that the majority of individual animals in any ecosystem are going to be herbivores, not predators. No reason why they would gain any benefit from killing people.
Ghosting is a process that involves conquering fear so you won't secrete pheromones and be invisible to the Ursa. Wouldn't simply wearing a hazmat suit or something similar prevent pheromones from being released from a person's body be easier, thus rendering the whole Ghosting process unnecessary? Better yet, why not just use non-pheromone emitting robots to deal with the things?
For that matter, wouldn't a berserker be just as effective as a someone ghosting while requiring much less ability and training? The only pheromone they're cued to is fear, and humans naturally switch from fear to anger if the flight-or-fight response is triggered the right way. Given the movie features a famous Ursa slayer with "rage" right in his name you almost have to wonder if this was a plot point in an earlier version of the script.
How about recruiting a bunch of clinical psychopaths to kill Ursa? Ones with absolutely no activity in their amygdaloid bodies, so they literally can't experience fear in the primal sense that'd generate pheromones.
Never mind odor-proof suits or fear-suppression: the whole premise of "ghosting" eliminating the smell of fear-pheromones is garbage anyway, because the "smell of fear" is still a smell. As in, volatile chemicals which can linger around and on their source, whether or not said source continues to emit them. Just suppressing fear isn't going to make already-released pheromones spontaneously disappear, any more than relaxing after exercise so you cease to sweat will make you stop smelling sweaty from a workout. Kitai should've had to take a shower before he stopped being detectable to the Ursa, because he'd already been scared by it for a considerable time before he manned up.
Guns and other projectile weapons apparently don't exist in this universe. There's no reason to come anywhere near an Ursa to attack it. Even a stone age bow or spear would make a huge difference.
Worse is that they do, the intro shows at least one soldier with a laser rifle sort of weapon, yet on that whole space ship all they seem to carry are melee weapons.