I have successfully used the 2560 with your "AdaLogger" Shield, and have been quite satisfied with the results.
When I decided to purchase the "Ultimate GPS Shield + Logger", I thought the 2560 would be a good match for it.
I have been able to use the Serial Monitor to see the output of the GPS chip, but getting the GPS Shield to log data has been a bit more of a struggle.
My idea was to attach a 6-pin M-F Header to the GPS shield so that I can connect to the ICSP Header on the MEGA, and then disable MEGA pins 11, 12, 13 (by setting them as inputs). Chip Select would be designated as Pin 10 on the MEGA.
This has not worked, and I was wondering if anyone had a better solution.