The standard pagination and layout of the Gemara follows that of Daniel Bomberg's edition of 1520-22, which was the first time that Shas was printed as a complete set. (Earlier Jewish printers, including the famous Soncino family, had produced only individual volumes.) A notable difference is that Berachos has 66 pages as compared to today's 64; that change was made in his next edition, approximately 1526-39.
There have been editions where Tosafos (and even Rashi) were omitted, but it doesn't look like there have been any where they were replaced by other commentaries. See Marvin J. Heller, "Earliest Printings of the Talmud," and Edward Fram, "In the Margins of the Text."