Am I missing some UI tricks?

[Artaud]

For me the upgrade process goes rather quickly. I just add a "B" or "2" to the existing design name, if I have only upgraded engines. If I make more than one component upgrade then I choose an entirely different class name.

I retrofit some ships right away, but often some members of the upgraded class are on patrol someplace and not near a space yard.

I regard retrofitting as an option, not a requirement. My fleets often contain modern and obsolete ships.

Sometimes I will create a specialist class for old ships. Those obsolete frigates can still give you good service if you strip out the weapons and install point defense cannons, or drone bays, or satellite bays, or supply bins, or medical bays.

[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.

[Possum]

I do it just like Q said. I use arabic numerals for combat ships, changing to a new number for a major upgrade, or adding a lower case letter suffix for a minor upgrade.

I do support ships the same way, but I use roman numerals for them.

I am a big, big upgrader. I build frigates with a repair bay and 2 engines, and leave them sit at major bases for fast repair capability. It's not at all unusual for me to have a per-turn repair capacity of 40-50 systems at a forward base.

I tend to build bare-bones combat ships, using only the absolutely essential systems - engines, sensors, weapons, armor, shields. For this reason, I build a lot of support ships, and I tend toward somewhat specialised support ships.

To a certain extent, this helps with upgrades, as the systems that need upgrading are often on a support ship, rather than on the combat ships themselves.