I think you're overlooking its usefulness it situations other than first turn. Now, it's not great in every deck but here are some situations where I find it helpful...
I agree with some of your points, but I do wish to elaborate and/or offer counterpoints.
1. Donking Swablus: Stunfisk can donk Tynamo but Emolga can donk Swablu. However, this requires Lightning energy.
Emphasis added to cover my main concern; having the Energy to pull it off. If I an burning a
Blend Energy WLFM (which my deck would have to, I don't know about what the more experienced players are running), it really
needs to be for the win.
Otherwise, it is still handy handy but could backfire; I don't want to whiff on an important Retaliate later (for example) because I ran short of
Blend Energy WLFM. This is less of a concern for other builds, and even I have to acknowledge "...but it was for a Prize, and now that is one more
Swablu that must be recycled and played before it can Evolve."
So let us contrast that to taking out an early
Tynamo with
Stunfisk. You can't do better than a first turn win with either, but in a more sustained match, taking out a first-turn
Tynamo hurts more than taking out a first turn
Swablu; with the former you're impeding Energy acceleration for a deck
Empoleon is Weak to, with the latter just lowering max damage cap for a Type neutral deck.
This is mostly "Theorymon" so definitely correct me where I am wrong (for example if
Garchomp/
Altaria is a
critical match-up).
2. Promotion: Whenever my active gets KO'd and I have Emolga on the bench I promote it. With free retreat cost it allows you to play out your hand before deciding which pokemon you're going to attack with. This can be invaluable if you need to draw "the right card" to return a KO.
This also allows
Switch to remove effects of attacks, and all of what
deashira said plus that can prove very, very valuable.
3. Decoy: Sometimes you're not ready to go on the offense this turn but you don't want to take damage on one of your core pokemon. Emolga is almost always the pokemon you prefer to lose. Using it as a decoy forces your opponent to use up valuable resources (Pokemon Catcher) if they want to attack a real threat.
The 90 HP is an important concern, since it is (for example) a bad thing against
Darkrai EX, where you just set-up them to get a Prize while hitting something important for 30. Of course, I may be over (or under) analyzing things again:
Darkrai EX isn't going to OHKO an
Empoleon or "follow-up KO" one that has just 30 damage on it without help.
I guess I am just concerned about an "easy Prize". I've lost matches (in more than just my
Empoleon builds) because my opponent has made good use of that
Emolga on my Bench. As a long time player, I have to remember that cards with similar uses (that is with respect to the free Retreat) also existed in formats where they were hard to OHKO:
Jungle Scyther had 70 HP in a format where that was
hard to OHKO, and the
Neo-era Baby Pokémon had the Baby Rule protecting them while Active (and an effective OHKO on the Bench required complicated combos).