I chose the third one because, of the three, it's the trope least familiar to me among (gaming) adventures I've ever run/played/read. I've experienced a fair number of lost jungle civilizations and desert temples, but not so many abandoned cyclopean cities.
I think all 3 are really cool ideas. I voted for no. 3 though because I think there is the scope to do something really cool in that design space with a dungeon sized to Huge inhabitants rather than Medium inhabitants.
PCs could be ambushed by monsters lying flat on a table 3x normal size. Opening doors require Athletic checks, etc.
I went with #3 as well for the reasons put forth by @FrozenNorth. You have opportunity for a more alien, unique exploration (drawing a blank on the adventure name, but ran a published Paizo module years ago dealing with a flying town that no longer functioned; party found one piece of the advanced tech to make it fly again and future adventures could be made up by the DM to find the rest...who doesn't want their own flying city??).
I've done #1 several times; although with not-intelligent apes (based it loosely on Michael Chrichton's 'Congo" novel). And with evil dwarves, a mad elephant-ish demi-god, prehistoric lizard archmages, dimensionally lost Romans, and other assorted oddities. I was always a sucker for 'lost city in the jungle' stories...