I actually own both a 99 Valkyrie Standard, and an 05 Rocket 3.
The pros of the Valkyrie is that it is a tried and true motor, same motor that was put in the older gold wings, with the exception of having 6 carbs and more power. The engine is silky smooth and has plenty of power and was dubbed the worlds first power cruiser. I am pretty sure it also took cruiser of decade honors at some point.
Cons is it is carbed, and if you put pipes on you can not just hook it up to a computer and tune like you can the rocket. You have to change needles in the carbs which is really not that hard, I did mine myself.
The only problems I have had with mine is a starter switch, I now carry an extra in my bag and it can be changed in about an hour. I have 70 thousand miles on mine and would not hesitate one bit to hop on it and ride it across the country tomorrow.
It is a super reliable bike, and the only catastrophic failure I have ever heard of has to do with the petcock failing and causing the engine to hydro lock. This of course is a huge problem if it happens, but very few have actually had this happen.
You can put a pingle petcock on it and manually turn off if you want to cure this, and some people have. I have a belly tank on mine so it is not subject to ever having this problem with my current setup.
Gas mileage is about the same between the 2, and riding the Rocket is like riding a supercharged Valkyrie.
If you want to see how smooth the Valkyrie motor is, check out this link
YouTube - Honda Valkyrie Nickel Test
It is called the nickel test. Pretty impressive how well built the motors are on the Valks.