The introductory note (in your second link), from Sefer Kerisus by R. Shimshon of Chinon (a prominent Tosafist), explains that the 32 middos are indeed an amplification of the 13, but that (a) not all of the former are universally accepted, (b) some of them aren't really middos (exegetical methods) at all, but amount to a different kind of peshat ("as if it were written openly"); and (c) some of them are used only to understand the meaning of the verses, whereas R. Yishmael's 13 middos are all used specifically to derive halachos.
It's important to study a bit of Gemara every day, and learning R. Yishmael's beraisa fulfills that, "for Midrash is like Gemara" (Shulchan Aruch, Orach Chaim 50:1). Tur adds that this one was chosen because it is the introduction to Toras Kohanim (the major halachic midrash on Vayikra, also known as Sifra), which presents most of the laws of korbanos - indeed, many of these middos are used to deduce details of those laws. So it fits well following the daily recitation of the offerings in the Beis Hamikdash.