I think the reliability issue is really a compatability issue with the newer engines (V6) in 1997. A few posts recently discussed that as well. They are both good transmissions and engines. The 1997 problem was fixed and is also mentioned here somewhere.
1994 E320 Wagon (Died @ 308,669 miles)
1995 E300 Diesel (194,000)
1999 E300 Turbodiesel (244,000 miles, dies at 255,000)
2006 Toyota Tundra SR5 AC 4X4 (115,000 miles)
2011 Audi A4 Avant (129,000 miles) hate this car!
BMW 330 xi 6 speed manual (100,034 miles)