I currently own both the 1Ds3 and the 5D3. To be perfectly blunt, I am having a hard time adjusting to the 5D3. For me (I'm using the 1Ds3 for 5 years now) there are a few drawbacks when using the 5D3.
- weather sealing (this is something I am uncertain about. how sealed is it really? with the 1 Series I am certain that they outseal me.
I haven't had a single Error Message or anything of the sort since i got the 1Ds)
- exposure indicator (in viewfinder). on the 1's it makes perfect sense, it's on your right side, going up and down. with the 5D on the other hand you'll get it at the bottom going left and right...why canon? seriously!
- on the 1s you are getting a little lever that closes the viewfinder so no light will enter from the back (landscape, long exposure etc) which i find quite handy.
- for me, the 5D doesn't feel comfortable in my hands. I'm used to bigger cameras and I find it too small.
- black af tracking points on the 5D...meh
- zoom button on the 5D
- mode dial...so unnecessary! give me buttons like on a 1D.
- power on. can't reach when you're 1hand holding the camera...needs 2nd hand.
- battery life; yeah you just cannot beat a 1Ds3
I could go on and on. But there are also some good things about the 5D.
- AF speed and accuracy is pretty nice.
- back screen is lovely.
- the silent mode is silent...really!
- it's lighter than the 1Ds (can be a plus or a drawback depends on you)
All in all those are two entirely different cameras. I wasn't aware that the difference would be this major. But hey, maybe it's just me. If you do alot of landscape things and need to travel light, going with the 5D might be a wise idea. If you want to be sure that the camera will do repeated work whatever environment or weather (also taking alot of bumps and knocks) the 1D series is more what you want to go for. maybe the 5D will be pretty tough...who knows...it's not out long enough to draw real conclusions (for me).
my 2 cents
ps: drawbacks of the 1Ds3 are: not as good an AF system as the 5D3, screen you cannot use for focus checking, silent mode is not silent, no iso steps between 1600 and 3200.