Sure Godzilla vs Gamera is a popular matchup among fans. But compared to Godzilla vs Kong, that's a fundamentally better pairing.
Gamera is a Godzilla clone, and because of that it becomes a mirror match of two invincible kaiju reptiles.
Compared to Godzilla vs Kong, there's a much bigger and drastic contrast. You have basically a reptilian nuclear bomb vs an ape with near human-like intelligence and doesn't rely on crazy flashy powers.
Godzilla vs Kong also objectively holds more weight culturally. The ultimate clash of Eastern and Western icons. Compared to Godzilla vs Gamera which is solely a battle of two Japanese icons, one of which nobody outside of hardcore fanbases care about.
The best comparison I can give in regards to an actual fight itself is Hulk vs Wolvarine. It shouldn't be a matchup at all, and yet its the most iconic cross match in Marvel comics. Compare it to something like Hulk vs Doomsday, would it be cool? Sure, but it would never hold a candle to Hulk vs Wolvarine despite it being a more fair fight on paper.
Because when you have two beings that are very similar it might be logical to have them fight but when you have two beings that are nothing alike at all they're usually regarded as some of the best matchups of all time.
Buts thats just my opinion.