Norm beat me to what I was going to say...but I'll say it anyway. With my professional experience with cage ABS systems, I feel most should not be allowed on the road. The first thing I do to one of my vehicles, if equipped with ABS, is to disable it. Most cage ABS systems are terrible, especially American vehicles.
BUT...I think bike ABS systems, especially Honda, seem to be very problem-free, absolutely invisible (meaning no strange handling quirks), and it does it's job without you knowing it did it...making it a very good system.
Linked brakes: I like my linked brakes, and they do a great job of stopping the bike. Yes, they add complexity to the system, but with basic maintenance, they should continue working well.
That said...personally, I wouldn't bother paying extra for ABS, but unlike a cage, I wouldn't be afraid to have it on the bike if a good deal on an ABS bike came along. Between the two bikes you mentioned, I like the '03 because of price; and the '06 simply for the adjustable windshield, which I use all the time on my '06, and wouldn't go without. Our weather constantly changes, with a 40 degree tamp. range and sun or rain all on the same day, so being able to block the elements when needed, but lower it for additional airflow when the temp rises, is important to me.
Good luck with the purchase...only you can decide what is important to you, and decide how much its worth paying for.
Jim