I'm not a believer, but I think I can play Devil's advocate and give you the lines I would have given as a believer on these (I'll answer as if I'm Christian with a semi-fundamentalist Biblical interpretation):
Is there a reason why "god" gives special treatment to humans and not other species of animals?
God doesn't give a reason, but he decided to create man in his own image... some take that to mean that man is like God in regards to the spiritual nature of man. Because of this, God gave man dominion over all of his creation.
And if god is against homosexuality, why would he create homosexuals?
God didn't make the gheys, they're an after effect of original sin.
Basically, God's initial creation was perfect and without sin, but once Lucifer helped lead Eve into sinning, sin had a negative effect on everything. Sin, mixed in with creation, devolved God's creation and continues to do so. People in the Bible reportedly lived for hundreds of years, whereas now we're lucky if we can get to (or close to) ten decades old. It was at this time that nudity became something to be ashamed of (or at least modest about), and it was probably around the time that carnivores diverged from creation and started eating other animals. The point and time that all animals were vegetarians is known as the original "age of innocence."
Why would he make it so that people sin and go against his will?
Free will was one of the first things he allowed man to have. Also, Eve was baited by Lucifer... who then baited Adam.
Why was "god" so involved with mankind at the beginning times but hasn't even done any of his magical things and floods during more recent times?
That was before God came to Earth as a man, basically redrawing his contract with humanity, making it easier for his creation to get into Heaven. At the same time, God became forgiving, partially because he knew firsthand what mankind was enduring under original sin.
Why would god create so many regions of people who believe in completely different religions?
Partially, that stems back from God's allowance of free will, and regionally, the resulting infidels are products of what happened with the sinners of the Tower of Babel.
Why does he make all these "sinners" doomed from the start?
Technically speaking, babies and kids (innocents) would go to Heaven if they passed away. Jeremiah 1 talks about people being sanctified before they're born, so they get a free pass.
Having said that, we're born into a world of original sin, so when you reach the age of reason, you should do away with parts of your reasoning and have faith. So basically, sinners aren't doomed from the start, but they doom themselves even though God knows they're doomed to begin with (if they were raised in a non Christian country or something).
And if there is a god, why would he wait millions of yours to gain some legitimate followers (the jews)?
Ah, but God was directly involved with all sorts of people before the Jews... right from the very beginning with Adam, Eve, Cain, Able, and down the list . Then he went off and destroyed everyone that was alive that didn't believe, because they really, really should have.
However, God did leave a rainbow declaring a new contract with man, which was kind've an interim contract that lasted until he came to earth as a human, which may not make a lot of sense, but God is into contractual obligation.
Why would the creator of the Universe be fine with the paleolithic people worshiping their native gods?
He's not fine with it! God was a jealous God since the Old Testament, and even God-as-Jesus told everyone "I am the way, the truth, and the life. No one comes to the Father except through me." So you either believe or spend an eternity in either the Lake of Fire or just without the presence of God at all (that part's not entirely clear).
Wouldn't he had made it so that everyone was a follower from the get-go?
That's probably how it was before Eve screwed it up for everyone.
I'm pretty sure there was no concept of worshiping Jehovah (the christian and jewish god) until sometime in 1400 BC.
Historically, you're probably right, but the Biblical timeline is much different from your secular history books.
/end Devil's advocate mode