Ni, ND.
I have a few minutes now, so I'm going to give you my thoughts. Since they are from the perspective of a believing Latter-day Saint, I'm going to respond with comments stated as if they were fact. Knowing that you believe differently, please just assume that each of my statements begins with the words "I believe, and my religion teaches..."
non-duality said:
1. Less than 50% of all embryos will reach birth. Will this souls never have an human existence? Would that be justice?
This is only an issue if you believe the human soul (I'm assuming you are using this word as I would use the word "spirit") existed prior to its birth. I don't know of very many people who believe it did, but I am one of them. God created us spiritually before we were ever born and that we existed in His presence -- in spirit, not corporeal form -- for an unspecified amount of time. We have existed as cognizant entities for perhaps billions of years, during which time we had an existence of sorts. We had emotions, intelligence and free will. We just didn't have a physical body, but we existed nevertheless.
2. Can there be an eternal punishment for a short time life? Would that be justice?
No and no. There will be an eternal punishment for some, but not for a large proportion of us, and this punishment will not be based solely on 70 or 80 years of mortality. It will be based on our decisions and behavior in our pre-mortal life (as I explained in answer to your first question), our mortal life, and a post-mortal existence during which our dis-embodied spirits will continue to be able to learn, grow, make decisions and progress. We we exist in this state until our physical bodies are resurrected and reunited with our spirits. This life is extremely important, but it is not the only part of our existence on which we will ultimately be judged. Because each of us has a physical body, we are subject to disease, injury and death. We are also subject to temptations of the flesh that we did not experience in our pre-mortal existence and will not experience as we await the resurrection. During this port-mortal period, barriers to our understanding will be removed, as will a lot of our "cultural and environmental baggage."
3. How could there be a hell as a place far from God as God is omnipresent? This place is just an illusion, but it's our illusion. And we only have to overcome this illusion.
Omnipresence is a word that never appears in the Bible. God is never said to be everywhere at once. On the contrary, He is repeatedly said to be "in Heaven." Your assumption makes sense only if you also believe there is no Heaven (as I realize is probably the case). But for anyone who believes in a Heaven, it is entirely reasonable to believe in a Hell, as well. Every state of being has its opposite, and Hell is the opposite of Heaven. If Heaven does exist, so must Hell. If Heaven doesn't exist either, then my argument falls apart. If Heaven exists, yours does.
4. As God created man in his[/her] own image would God condemn his[/her] own images and be happy about this. Wouldn't he[/she] be more like the shepherd who will not rest until the last sheep is found?
Of course God wants all of us to return safely home, but the fact that He gave us our free agency (i.e. free will, free choice) guarantees that He will lose some. The fact that, by the time His entire plan has played out, everyone will have been given ample opportunity to make an informed and impartial decision as to what he wants to believe and how he wants to behave. It is because God loves us so much that He is going to do everything in His power -- except take away our free agency -- to make sure we have every possible chance to be "found."
5. If God is almighty, will he[/she] forsake the wish of a soul to come once more into human existence. For example in order to help others? And if God does not allow that, why? Because it is not possible to God???
God will allow with a far greater opportunity -- that of progressing forever, having the potential to ultimately become as He is. Depending upon how we live, (in our pre-mortal, mortal, and post-mortal/pre-resurrection existence) we will be in a position to help others, for instance, in ways more far-reaching than we can even begin to imagine. We are gods in embryo. I'd rather just progress eternally as myself than return to this same earth over and over again as a different individual.
I'd be interested in your responses.
Kathryn
) are exempt. 
