Under these caveats:
-Ignoring openings
-Ignoring "World of Pokemon" Segments
-Counting Orange Islands as part of Gen 1 and Battle Frontier as part of Gen 3
-Acknowledging movies and "main anime" specials (that is, I would count Legend of Thunder but not Twilight Wings) that aired during those times, but keeping track of when they "actually" appear in the anime regardless
-Not even bothering to acknowledge the "side game" specials like Mystery Dungeon
-Ignoring Mastermind of Mirage Pokemon since its just like. A weird spot in general.
Gen 1
As you'd probably expect from only having one set of critters to draw on gen 1 mostly didn't have this problem. That said
- Articuno. Ignoring the stone carving cameo in the first 3 episodes, first appearance was Movie 2. If you want it to show up in the anime proper you had to wait until the Johto anime
- Zapdos. Uhhh actually I wasn't sure if I should count the big Zapdos animatronic from the Island of Giant Pokemon; like its not Zapdos but its not....NOT Zapdos....? Otherwise its similar to Articuno; Movie 2 and then had an episode in Johto
- Mew. Obviously it was in Movie 1, but what about the normal anime? Well. That took until Diamond & Pearl where it showed up in a Boss Fantasy Sequence! ...if we don't want to count that then it was the Sun & Moon anime.
Moltres got to show up for the olympic torch stuff (its expressly Moltres this time) and Mewtwo had a string of episodes where it's setting up the movie.
Gen 2
Johto felt like it went on for so long so I really expected this to not be an issue.
And yet!
- Typhlosion. As you mentioned, kind of an interesting case. Its ONLY appearance was Legend of Thunder until the Hoenn anime (where it showed up 3 times!). It's very odd for a starter to be like this; all the other gen 2 starters showed up several times throughout Johto. Again I don't think there's necessarily an issue counting the "Specials" as part of the anime (especially from this era where they are meant to be canon), but I thought it was worth listing regardless.
- Togetic. There are no caveats beyond World of Pokemon stuff in play here, it simply did not show up until the Misty cameo episodes in Hoenn. And then made one (1) other appearance in Diamond & Pearl. Wild!
- Flaaffy?? Outside of the third movie it was in Legend of Thunder; it otherwise had to wait until the Hoenn anime.
- Porygon2. Lol.
- Celebi. After the 4th Movie it had a Ritchie special (in the Advanced era) and after that it would show up in the Battle Frontier
Flaaffy & Typhlosion make a good case for just counting the specials with no caveats. But it's fun to point out so I'll keep doing it
Gen 3
- Latias. After Movie 5, it had the Post-DP Brock Special episode. Now normally I would just straight up call that a normal episode of the anime, because it just...aired. Normally. In the time slot. "Legend of XYZ" is in a similar boat, but is treated normally in the west as an example. But the episode never gets aired outside of Japan! And Latias has only appeared in other special stuff like the Mega specials. So it seems worth having here.
- Latios. After Movie 5 it had to wait until Tobias' Latios to show up in DP.
- Rayquaza. After Movie 7 it had to wait until a later DP episode.
- Jirachi. After Movie 6 it had to wait until BW.
All things considered Gen 3 did really well for itself. I really don't get why America never brings over the "wrap up" specials; the only one they've bothered with was the "Legend of XYZ" episode i mentioned earlier. Curious why Jirachi took so long to show up, though. Its appearances are very sparse even today.
Gen 4
- Porygon-Z. lmao
- Giratina. The only reason I'm listing this is because I waffled on Zapdos & Mew. Giratina showed up twice in the DP anime once as an illusion from another Pokemon and another time as part of a boss fantasy. It's otherwise not showed up outside of a Movie.
- Manaphy. Had to wait allllllll the way until the SM anime.
- Arceus. After its movie (and a brief cameo of its mandala in the Galactic climax) it had to wait until Journeys. Long time coming on this one.
Not too shabby from gen 4. Surprising that Phione, Darkrai & Shaymin all got DP episodes but not Manaphy, though.
Gen 5
- Klang?! Wha?? It was in the Victini Movie and then....a Genesect movie tie in that never came to the west. I forgot that movie even HAD a tie in. It did at least have characters from the anime so I guess its in the same boat as Latias, but...what a weird Pokemon to be like this. It's still not shown up in another episode!
- Cobalion. Only showed up in the Keldeo movie.
- Terrakion. Only showed up in the Keldeo movie
- Virizion. Only showed up in the KEldeo movie
- Kyurem. Movie only
- Keldeo. Only showed up in the Keldeo movie
Klang....
Gen 6
- Diancie. Movie only. Gen 6 did have some shorts for it & Hoopa as part of movie ins, but I'm not counting those anyway
- Hoopa. It showed up proper in Journeys after its movie.
- Volcanion. Movie only. Didn't even get a short for it...
Gen 6 benefited a lot from being a tiny generation.
Gen 7
That's right gen 7 has absolutely no issues. Every single gen 7 pokemon from Rowlet to Melmetan showed up in the SM anime proper.