I have a Cronus Pro & like it! Has a good smooth ride, corners like it's on rails, and the hidden fender mounts are cool. As you know, the frames are all the same layup. One reason to buy a Pro or Ultimate would be to get the lighter wheel set- since the front hub is proprietary it makes it harder to sell if you want to upgrade.
(disclaimer: my first frame cracked strangely, as noted here, but it was replaced w/o hassle.)
What is the saying, Don't buy upgrades, ride up grades.
I really like the Cronus since it sort of fills its own niche, a comfortable geometry, flanged hubs, and fender mounts, but I think it is is laughably overpriced.
I honestly think that 105 is a completely serviceable group, and the jump from 105 to Ultegra is in no way worth $1000. What do you get for your $1000? Ultegra, some marginally better contact points, and a "better" Bontrager wheelset.
I actually have the 2011 105 on one bike and 2011 Ultegra on another, when well adjusted, I see almost no difference other than maybe some weight.
As for the wheels, both have the flanged hubs that is the Fisher road bike trademark, but neither of these are going to be your race wheelset (if you ever race). As a training wheelset, I doubt one will seriously outlast or outperform the other.
Finally with the contact points (handlebar, seat, and to some extent stem and seatpost), a lot of people ride the stock stuff for years and years and love it, but I would venture to guess that most people dropping $4k on a bike have a preference (or will eventually). You may want shorter drops, a longer stem, a setback post, or a different seat.
If you really, really want the upgrade to Ultegra, I would talk to your LBS and ask them if they would quote you on upgrading the group. I guarantee it won't be $1000.
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