Dr Funkenstein (who is, if I'm not mistaken, a professional scientist with an advanced university degree) decided to take a swing at the challenge in this comment:
As a good example of a reasonable evolutionary extrapolation for common ancestry:
God could have made humans with 100 chromosomes and primates with 24, rather than 23 and 24, respectively. He could have made it so human chromosome 2 was nothing like Chimp, Orangutan or Gorilla chromosome 2. He could have made it so there were no telomeric repeat sequences in the middle of human chromosome 2. In fact, he could have made our genetic material totally different from that of chimps. You know, so there'd be no doubt we're not related to primates by common ancestry...
Honestly, I don't know if I ever imagined the case could be so weak!
All he's done here is ask a question about God, which he has no way to answer either way.
1) Maybe God just wanted to do it that way.
2) Maybe God wanted to deceive HIM.
3) Maybe God sent "upon (him) a deluding influence so that (he) will believe what is false, in order that (he) may be judged who did not believe the truth, but took pleasure in wickedness" (2 Thess 2:11-12).
4) Maybe it gives God glory in some presently inscrutable sense to make the chromosomes that way.
5) Maybe in the way that God set up our bodies and biology, it made sense in some way we don't yet know to make the chromosomes that way.
I'm not saying I believe all of those (#2 comes to mind), but they are logical possibilities.
Appealing to incredulity is no way to convince the skeptic. Talk about a double standard! You wouldn't accept the same from me. How many times have we seen atheists and evolutionists mock the naive Christian who argues thusly: "But, the universe is just too complex and improbable for it to have arisen without a First Cause!"?
The irony is rich in any case - Dr Funk does not believe in a grand design from a Grand Designer, yet here he is offering pointers to the Designer as to what it might take to make the Designer's existence more plausible in his mind. I'm sure God is taking notes.
Where is the overwhelming evidence?
More to the point, does this even get close to responding to the question?
Finally, I'd just note that my request is presuppositional. Don't bother throwing data at me in the combox - if you can't justify extrapolating into the unobservable, into Deep Time, on the presuppositional level, data is useless.
(On a side note, I'm sorry that Dr Funk might not be around to deal with this, but the combox remains open to perpetuity, so after his upcoming 2-week vacation he might wish to set the record straight and actually answer the question.)