The 6.3 handles better, is quicker, more stylish, and overall is a far funner car to drive.

The 6.9 is more practical, has a slightly (perhaps 5 MPH) higher top speed, is more modern in several ways, and is easier to live with as a daily driver.

Neither car is hard on transmissions. 6.3s can be a bit hard on rear ends if abused, but this takes many many burnouts. Both are quite reliable and have a bad rap as to cost and reliability. The reason that they tend to be expensive to maintain, is that much of the required maintenance was never performed, and over the years this has piled up to the point where it is required. Once these cars are repaired, the repairs are good for another 10-20 years. The suspension on both cars is a good example of this.

The air suspension of the 6.3 is both cheaper to repair and superior to the hydropneumatic suspension of the 6.9.

I speak from authority -- I had low-mileage examples of both cars in my garage for around 4 years, and continue to drive the 6.3. I replaced the 6.9 with a 1994 E500.

Cheers,
Gerry