To avoid the dreaded "unwanted carrier TF reaction toward enemy carriers resulting in losses and cursing too horrible to mention," you have to form a surface TF and order the CVTFs to follow it (everybody on do not retire and do not react). It's an awkward workaround, but it works every time.
I also hope that this is addressed in CF, but I've gotten used to the technique, and it has the added benefit of sometimes drawing off enemy airstrikes that were intended to put gaping holes in your carriers and resulting in gaping holes in a few surface combatants instead. I probably won't change tactics in any event (and I intend to look at CF closely before buying it, as I have not seen enough information on it to decide whether it will be a sufficient upgrade to UV to justify the expense).
My real problems with UV (and WitP, for that matter) have been that they do a poor job of defining your role as a player. In UV, for example, you have exact control over altitude assignments for air groups, yet you have no ability to give orders to strike groups setting priorities for naval targets. Furthermore, your bombers can fly outrageous distances to hit relatively worthless targets, when you really want them to beat up something much more threatening and close at hand (this was ameliorated to some degree in WitP, of course, with maximum range setting, but still...)
Did I mention what a PITA it is to see your TF commanders tossing their orders over the side and running like cowards from enemy carriers that haven't even been spotted and are often a thousand or fifteen hundred miles distant? Yes, you can give "do not retire" orders, but that often affects the execution of missions (minelaying and bombardment, for example).
Personally, I think any commander who disobeys orders and makes a run for it in the face of the enemy ought to be summarily hanged from the highest yardarm in the fleet.
Put my faith in the people
And the people let me down.
So, I turned the other way,
And I carry on anyhow.