It's fairly well-known that the gym leaders throughout the Pokemon franchise pick their teams depending on how many badges a challenger has. But there are some Pokemon that could certainly be swapped out to make for a better experience.
The Johto region has its fair share of questionable gym leader teams. Of course, this doesn't mean that Falkner should pulverize the player with a Dragonite or that Clair should replace her Kingdra with a Dratini for an easy sweep.
These replacements should be added relative to where the gym leader's team is already level and difficulty-wise when the player challenges their gym. The goal is to make their teams a better fit, not to make them easier or harder deliberately.
Note: This article is subjective and reflects the opinion of the writer.
Three replacements for Johto gym leaders' Pokemon
#3 - Clair and Aerodactyl
Dragon-type Pokemon are a rarity in Generation II, with the Dragonite family tree and Kingdra being the only Dragon-type Pokemon in the entire Generation. Despite this, the Johto region still has a Dragon-type gym as its eighth and strongest gym.
The original Gold, Silver, and Crystal team was extremely lackluster, with Clair having three Dragonair's and a Kingdra. While still a difficult fight casually, the horde of Dragonair's was somewhat confusing and not an overly enjoyable experience.
Replacing one of Clair's three Dragonair's (or two in the case of HeartGold and SoulSilver) with an Aerodactyl provides a decent deviation in the fight without just adding Dragonair's evolution, Dragonite.
Aerodactyl is a Dragon-like Pokemon with a vast move pool, such as the elemental fangs and several Dragon-type moves that would give it all the variety to fit as a threat in the eighth gym leader's team.
Clair also happens to use an Aerodactyl in her rematch with the player in HeartGold and SoulSilver, so at the very least, it's confirmed that she would consider using one.
#2 - Jasmine and Magneton
As is the fate of many gym leaders, Jasmine also possesses many of the same Pokemon. It can't be helped too terribly much since the Steel-typing was just introduced in Generation II and not many Pokemon had that type yet, but there could still have been an improvement over only using two Magnemites.
Replacing one of Jasmine's Magnemites with a Magneton doesn't change her team's overall power that much but does manage to increase the diversity of the fight. The only other potential option would be to include Forretress. Still, with a Steelix already on Jasmine's team, her already astronomical defenses would become more of a chore to deal with than a challenge.
Magneton provides a better mix of diversity and challenge compared to Forretress or a second Magnemite. A second Steelix is hilarious to consider but totally out of the question.
#1 - Morty and Misdreavus
Morty is the gym leader in Johto who needs the most help. This poor man has four Pokemon, two of which are the same and all from the same family.
Once again, it can't be helped too much since there were only four Ghost-type Pokemon in Generation II. But if there were four Ghost-type Pokemon in Generation II and Morty had four Pokemon, wouldn't it make sense for him to have four different Pokemon?
In short, Morty's second Haunter should be replaced by a Misdreavus. It was a pretty decent Pokemon in Generation II, weak only to the somewhat rare Dark-type and almost nonexistent Ghost-type while being outright immune to the prevalent Normal-type.
It may have lacked for decent damage output and defenses, but Misdreavus would fit in just fine among Morty's team and would have been a nice change of pace from the swarm of Haunters players faced in the fifth gym.