Current clincher rims are made for 25mm tires. Putting 28s on them will result in a wider tire profile. The current setup with Ultegra calipers it is tight getting the tires through the brake calipers with the tires inflated, and apparently unlike a some other riders I do this pretty regularly, some weeks every day. If the tires were mounted on rims designed for 28s the rim would be wider, the caliper setup would start wider and they would probably make it though with the cams open. I'm also not sure my frame has clearance for 28s in the rear. It is pretty tight.
As noted above, I ripped a sidewall on my ride a few days ago, new Conti 25s are on the way so I'll be a couple of thousand miles before I revisit this.
Thanks for the feedback on the ride though.
When it comes to 25 vs 28, the rims are (realistically) neither here nor there unless you're looking to wring every fractional gram of drag from your aero profile. Frame and caliper clearance are very real concerns, but running 28mm tires on rims "made for 25mm tires"? Not an issue beyond how much as they'll affect clearances.