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5D3 has 6fps, 1Ds3 does not
1Ds3 has voice memos, 5D3 does not
1Ds3 might have workable AutoISO, 5D3 does not
5D3 has instant jump to 100% view (so convenient and saves a lot of time)
5D3 has much nicer UI (IMO anyway)
5D3 isn't a damn brick , 1Ds3 is
1Ds3 has replacement viewfinder screens, 5D3 doesn't
1Ds3 has less banding junk and a bit less read noise at ISO100-200 (but the DR is already worse by ISO800 and probably even ISO400 on the 1Ds3, noticeably so by ISO1600-3200)
1Ds3 is less color-blind under natural lighting (hard to say how much and in what ways and when...Show more →
I played with auto iso on the 1ds3 when I first got it 5 years ago. It would have been useful for BIF, but I never liked the way it was implemented. I don't even recall now why. Had something to do with what part I could keep constant. I wanted to keep the shutter speed high as I recall.
I also played with highlight priority and never liked that either. The 1DS3 buffer was too small for sure, I missed many fish pick ups when it filled too soon. The burst was fine however and I thought the AF was fine. It was a competent BIF camera.
But I had a 50d which had more buffer and faster burst and higher pixel density. But battery life in cold weather was horrible and in the end, the better high ISO, and better af of the 1DS3 trumped pixel density. I ended up using the 1DS3 for birds.