Surprisingly, for the B-17s legendary toughness, the B-24 had a lower loss rate than the B-17 over Europe when flying in the Eight AF.
This is true even when assessing the two aircraft over the same operational period. Yes, the B-24 was a relative late-comer to the ETO compared to the B-17, and the Flying Fortress took the lion's share of losses during the dark days of 1942 and 1943. However, on a mission-to-mission basis, the B-24 was statistically less likely to be shot down.
Loss rates for 8th AF bomber groups that arrived in the ETO after December 1943:
B-17: 1.42% per sortie.
B-24: 1.11% per sortie.
The B-17 was more survivable when damaged heavily - hence its reputation for toughness and the fondness for the aircraft by its crews - but it actually tended to lose out more heavily in an operational comparison. The B-17 was also more survivable when it came to a water ditching, another plus in its favour.
The B-17 had a higher ceiling than the B-24. It was also a more stable flying platform and was a much nicer aircraft to fly, both in and around the airfield and at high altitudes. The B-24 was notorious for being very difficult to manhandle about the sky, with very high control forces necessary and a tendency to be laterally unstable above 20-22,000 feet. There was a standing joke that you could spot a B-24 pilot due to his overdeveloped left arm muscles.
As B-17s were more stable at high altitude, their crews also flew tighter formations. This ensured better mutual protection against fighters. Combine this with the B-17's slightly better defensive armament scheme and its higher altitude and its understandable that the Luftwaffe had a preference for going after the B-24s.
I've seen it written that the B-24 was the best escort for the B-17, as the newer bomber flew lower than the Flying Fortress when operating, providing an easier target for flak and fighters. However, the B-17 seems to have suffered higher loss rates to flak than the B-24.
The survivability advantage of the B-24 lay in its higher cruise speed. Depending on the comparison of the various sub-types, the B-24 could cruise at anywhere from 10 to 30 mph faster than the B-17. When you're in a flak box, or being attacked by fighters, that speed makes a difference.
The B-24 had a marginal advantage in bombload. While the B-24 could technically hold almost twice the B-17s bomb load internally, in practice the two aircraft carried virtually the same load over both the ETO and the MTO. The B-24 only shows its advantage on longer-ranged missions (past Berlin). IIRC, the difference in the average bomb-load was about 200 lbs in the ETO.
The B-24 also had a minor advantage when it came to bombing. The B-24's roller style bombay doors did not upset the airstream nearly as much as the the B-17's downward swinging doors, which resulted in easier aiming for the bombardier.
EDIT: Found some information on bombing accuracy by aircraft type.
In 1944 B-17's averaged 15.2% of bombs within 500 feet of the target, while B-24s averaged 10.2% within the same distance. B-17s averaged 38.2% of bombs within 1000 feet of the target, while B-24s averaged 28.2%.
This is despite B-17's dropping from higher altitudes.
Part of the reason for this is the B-17's better stability, but the B-24s also dropped more often in poor visibility. As 1944 progressed, B-24s shifted from 12 abreast to 9-10 abreast formations, resulting in better accuracy for B-24s in the final three months of 1944.
Reading the USAAF report in 1944 bombing accuracy, and I'm astounded at how big some of the CEPs were. 8% of bombs dropped with visual aiming in good conditions in the year had a CEP of GREATER THAN 5 MILES! At a bombing altitude of 22200 ft, that's a error greater than the altitude the bombers were flying at!