Geez...that's a tough one. They really are two almost completely different bikes in many ways. For pure comfort on the road, you really can't beat the Ultra because of the TP, the updated HK stereo, more speakers, ABS brakes, new style frame ("better" handling), bigger tires. Nicer stock seat for sure. Some liked the '05 seat, but most end up changing it for something a bit more comfy.
The 103" engine on the '05 is not the same as the 103" on the new bike. The older 103" is proven and is a really good motor. The new 103" motor is also good, but different design.
The '05 SEEG has nicer paint, a bunch more chrome, and is a classic CVO bike. You can add the chrome to the new bike, but you'll never recoup your money on resale. If that's not important, then don't worry about it and make it your own. Even the SEEG doesn't have EVERYTHING, but more than the Limited with regards to chrome stuff.
The older bike has lowered (1") suspension front and rear...not always a good thing. The new bike has full travel suspension (13" shocks as opposed to 12"). To be blunt, all HD stock suspension sucks, but you don't know that if you have no basis for comparison. It's adequate.
My opinion: If you are going to use the bike primarily for touring, two up...I'd opt for the Ultra because of the creature comforts and newer frame. But, I'd have to do some things to it for my tastes. If both are stock with regards to exhaust systems, that'll be one thing you'll want to change almost immediately, both for a nicer sound and better performance. So, overall looks...the SEEG. Functional features...the Ultra.