-Regarding Leah/Ayla:-
Being that Gaea's Navel was NOT terraformed with the rest of the dragon islands in the El Nido archipelago, it remains chronologically possible that Leah's tribe has existed there apart from the rest of the world since 65,000,000 BC. However, Gaea's Navel was really one of the only islands in the the El Nido sea in 65,000,000 BC (nothing had been terraformed yet), and who knows how far away from the mainland. Even ignoring the sheer cliffs that make entry virtually impossible, I think it's highly unlikely that Leah came from a stock of people who had always been there.
Also, when mankind came in contact with the FF later on, they began to rapidly evolve, meaning, essentially, that's really not too possible for Leah / her tribe to have existed this long and have not evolved. Personally, I subscribe to the theory of the time gate in the Mystic Mts. If random animals / annoying jungle beat playing things wandered in there too, it would explain how Gaea's Navel got populated. That might also explain how Leah would be able to get back to 65,000,000 BC and birth an Ayla (as she says she will in .
-Regarding Lucca/Lucciana:-
After the optional 'Burning Orphanage' sequence, Luccia reads a letter to Kid from Lucca. She mentions that they were good friends and colleagues, and says something along the lines of Lucca being a genius who would have surpassed her [Luccia] in scientific studies had she not come to her tragic fate. So, they're definitely not the same person, just good friends who are both scientists and both have purple hair and both have very similar names and both wear glasses, etc. etc.
Unless...maybe...just maybe...Lucca grew her hair out and changed her name and adopted a fake accent and BECAME LUCCIA!. We never actually see Lucca's dead body or anything. All I recall seeing in the Burning Orphange is a pair of glasses on the ground. Hee hee.
-Regarding Frog/ CC's Glenn-
I really don't know what to make of this. I mean, they're clearly not the same person, unless frog was reincarnated, because we know of CC 's Glenn's origins; he is Garai's son and Dario's brother. He even looks like Dario, so it seems quite likely that they are legitimately related and that he was born around 1000 AD or so.
Still, I feel like if there wasn't supposed to be a connection at all, Square wouldn't have given them the same name, the same inferiority complex, similar outfits, similar swords, etc. In the end, they even kind of turn out the same. Frog gets changed back to CT's Glenn (according to the PSX ending), having made peace with Cyrus, whom he succeeded in a way. Likewise, CC's Glenn makes peace with Dario/Garai after death, and succeeds them as well. Both of them end of bearers of great swords of power (CT Glenn = Masamune, CC Glenn = Einlanzer) as well.
It's tough to say. Personally, I don't think they're the same person, but the similarities are too great to be coincidental.