Two parts to "intelligence" by human standards
There's really two things to consider in producing another creature like humans that visibly demonstrate their intelligence by manipluting their environment to suit them and assert some mastery (domestication) of lesser animals.
One of course, is actually having the brains and a complex means of communicating ideas besides "bad", "good", "i like that" and "i fear that". The other is the means of manipulating the environment, and tools. And we still don't clearly understand how this happened to us to be able to properly predict how another spinoff creature might reach the same point. We see signs of growing tool use in other primates now, but much of that is a result of them watching us do it ("monkey see monkey do"), and as such can't be relied on to make the type of predictions the show was aiming for.
Certainly ant and bee colonies are a clear demonstration of how an individual in a group can be an idiot and yet through signals sent by messenger individuals (utterly unaware of what they're carrying) the colony can show massive awareness and adaptation to situations in its environment. In other words, the colony shows signs of consciousness and individuality even as the individual insect shows none. The special decided to look at the extensions of such colonies in jellyfish and spiders.
I think another fault might have been ignoring the fact that our metal and buildings and trash would still be in some parts of the environment...it would have been nifty to see what might have evolved as a result of the situation of an abandoned city falling apart.
"It's not like all animals will grow really big if nothing killed them." -- not all, but some will, and if sticking your neck out gets you food others can't get, then long necks will likely evolve. The problem is that most creatures today eat grass (no need for a long neck unless the body is too tall like elk and moose) or climb up into the trees they eat from. For a turtle to evolve a long neck, it would have had to have found some reason to not have evolved grass-eating which is nature's current direction of things since grass is so prevelant (even giraffes can deal with grasses, though they prefer leaves).
"why would sharks suddenly have a need for bioluminescence" -- perhaps a lack of food on the surface of the oceans due to excessive heat or cold? Although some creatures (like cats) have been steadily gaining some degree of infrared heat-sensitivity to deal with the dark...
"remember how raptors hunt in packs and use logic" -- I still consider that speculation at this point...believable, but not enough to base an argument on...particularly not after having based a movie on it
"Also squid have existed for millions of years and have remained pretty much unchanged" -- I would agree with this assesment. some creatures have definitely shown an end-of-the-road aspect of their evolutionary existance (as in, they're unchanged from pre-dinosaur times) and I don't see nature trying again with the invertibrates as long as there are vertibrates who can eat them.
on the show's prediction of the elimination of mammals:
yes, the big cats are disappearing, mostly due to us hunting them or taking away their own hunting and breeding grounds, but the small cats, particularly the domestic cats, are tremendously well adapted hunters of small insects and rodents, and given that most mass-extinctions tend to take out the larger animals, I can't see the food supply of cats ever disappearing...and small cats aren't hunted by anybody (you don't get much eating a meat-eater, and nature knows that).
Right now, we're the biggest killer of cats (roadkill) and the biggest danger to their extinction (eventually we might get stupid and "fix" the last domestic cat and poof! no more cats).