Yeah Jay, thats right, I found it too dark and a tad sinister. It's not that I dont like it, just not my fave from the bunch, I like the light humor of the others.
I really liked the start, government base. finding the artifact and the chase after that. I liked the doffed caps to the older films (the ark in the wherehouse etc etc).
I also liked the nuke part, thought it was OTT but funny.
The development of where everything was, via the madenss that the skull gave to Prof OX, the conquestodors etc etc, the finding of the graves where the skull was.
And the end, it said why they destroyed it all as once it was returned they erased any thing that said why there were there.
I wasnt really struck on Mutt, but there was some good parts, like what Jay said, but the jungle paret with him was silly, good for the kids watching, but not my cup of tea.
Like I said to start there were some good parts and some bad, overall I liked it.
As for parts that you think are form other movies, I think you would be hard pressed to find an adventure film that didnt take from another.
If I went in expecting it to be "awesome and the best Indy yet" I would have left dissapointed but I didnt, I went into watch an Indy film and thats exactly what I got, happy customer.
"No pressure, no diamonds" Thomas Carlyle