Can anyone give me suggestion about Dubai city tour operator which also go to Atlantis Palm beside other places which usually take about 4 hours in one package?

Just do the on/off bus for Dubai-look for it online for more information. You can get it at alot of places and it has two different routes-blue and red. If you pick it up later in the day the first day it is good for 24 hours so you can do the other route the second day. It goes out to the Atlantis and quite a few great spots in Dubai besides a cruise on the river.

do a dune/desert tour.. our favorite experience.

You can do a desert safari as an evening tour which is beautiful-includes riding around in the sand dunes and then stopping at a "camp" in the desert for dinner,entertainment,crafts,riding the camels,etc. I believed the one I used was called something like Knight's safari tours.

I would suggest besides taking a desert safari, add a ride by the "Yellow Boats" which give tourist boat rides around the Atlantis, Palm and World Islands and they even have a super fun thrill ride.
Hope this helps!

I love this city tour specially one which starts in the evening..it's really nice to enjoy yourself with your loved ones....