[Suicide Junkie]

Indeed. Retrofitting is often not worth the time and money for small tech improvements...
Changing all your ships and queues over the instant you get a minor upgrade actually hurts your empire.

Consider the engine upgrade. The difference in cost of the new drive is about 20 minerals. This saves you about 2 minerals per turn per engine, given average-to-weak maintenance reduction in racial setup.

Each ship you retrofit costs you about 275 minerals per engine for ion drives, 400 minerals for CT drives, and more for higher tech drives.
If we consider going from Ion 1 to Ion 2, then you're spending 1650 minerals to retrofit the 6 drives.
Retrofitting will save you 12 minerals per turn.

In order to break even that ship must survive, and not have any further engine upgrades, for 138 turns.

In other words:
Never EVER upgrade ion 1's to ion 2's. Build new ion 2's, but leave your existing ion 1 ships alone.

While it may be convenient to upgrade those Ion 1's at the same time as you upgrade shields or weapons, it is expensive.
Shields and weapons, on the other hand, are almost always worth the cost of retrofits, since they improve your combat effectiveness.