It says in the Gemorra (tractate Megilla 29a) that says, "The houses of prayer and learning in Babylonia (connotes the entire Diaspora ) shall soon be moved to the Land of Israel." meaning that shuls from around the world will be moved to Eretz Yisrael once mashiach comes. doesnt this imply that Jews were meant to stay in the diaspora before Mashiachs coming and then we will go to Eretz Yisrael once he is here?

That piece of Talmud is not Halachic but homiletic and should not be literally understood. On a Halachic note there is a mitzvah to make Aliya and live in the land of Israel and Jews are meant to do Mitzvot even before Mashiach comes. In any event the passage speaks about the shules, not the people and it doesn’t mention when.