It's too much of a concidence that they found the princess at the same moment that some builders found the red rock for Seth's knife
Also, Tom Cruise as a human being apparently was stronger than a god, so he could escape the possession and save his blonde gf and his friend. That doesn't make any sense.
And, if the first choosen one could die, how come Tom Cruise cant?
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"Too much of a coincidence": No, I do not think so.
Dr Jekyll and his bunch are clearly on a hunt for these relics. And Tom was there because he had stolen some letter from Jekyll about this very location.
So it was in a sense a joined effort. Perhaps (and now I speculate a bit) the uncovered tombs below London gave a final piece to Jekyll on where to find the princess, and so he sends this letter (which Tom stole) to the blond chick and boom; each discovery was connected and bound to happen shortly after one another, just as they did.
"Tom was as a human stronger than a God": How so? He survived the plane crash because he was under some spell and so apparently protected, and in the rest of the movie he could take a beating like few men can.... but stronger than a God, I don't see this?? In the end of course he fused with a god and so gained powers from the beyond for his own control. This was essentially the story, I think. But before this??
"And, if the first chosen one could die, how come Tom Cruise cant?": The first one was killed before the ritual with the dagger finished. Tom finished the ritual himself and so gained godlike (mummylike) powers in the end.
However, before the ritual Tom did survive the plane crash and how? If that other dude could not survive being speared by the priests who imprisoned the Princess.... well, perhaps this is the answer. The Priests know their business and killed the first chosen one properly. Even Jekyll said they would kill Tom once he was merged with Set. In other words, Jekyll knew how to, like the Priests knew how to..... of course, I am stretching for explanations here, but the truth is that we do not know to what extend he was under her protection or how the priests could kill the chosen one in the beginning..... fact is they did. Another view could also simply be that she had been alive for millennia and so had gained powers and skills she never knew she had, and these powers helped Tom survive the crash...
"The Priests know their business and killed the first chosen one properly. "
This is unexplained in the movie. That's a possible logical explanation but it's not suggested in the movie. And before you say that the director wanted us to give our own interpretation, it didn't seem like intentional. Just things they forgot to add or they got wrong in the story. It fails to have consistency.
"She had been alive for millennia and so had gained powers and skills she never knew she had, and these powers helped Tom survive the crash..."
The same can be said. This is a plot hole the movie never clarifies.
"Tom was as a human stronger than a God".
With this i mean that he could avoid Seth influece to save his girlfriend at the end of the movie. That means Tom is a super human.
I understand that you are not a fan of the storytelling in this movie and that you find it failed to deliver. My post aimed simply to answer your questions with the knowledge from the movie, and this can be done to some extend as I argue above.
To me those issues you address are true but not really a problem in the movie or to a movie of this type - but each to our own. Ultimately it boils down to opinions. And though the greatest movies are usually everything but direct, you are correct in the fact that this is not such a movie and so perhas demands are more linear approach in its storytelling.
Anyway, plot holes they are not. In the strict meaning of the word.
A plot hole is when something impossible happens that cannot happen in a particular movie's univers. Your mentioned issues are not explained well, but impossible they are not imo. True plot holes are actually not that easy to find. Most issues are simply lazy writing or so-called goofs.
Although we could argue that when Tom survived the plane crash so should the lover in the beginning have survived the dagger attack. And therefore this is a plot hole? However, the fact is that the lover died and as per the dialog of Dr Jekyll we learn these demigods are not eternally immortal... so simply by the virtue of the story presented to us, the univers in this film allows for deaths under certain circumstances... not explained, but not completely ignored either... I will grant you that this could tangent a plot hole... although easily fixed with a simple remark liked; "... she has become stronger than she ever was...". Imo this is exactly what the movie shows us and so I do not need this line be spelled out.