Your question is asked by no less than the P'ri M'gadim (OH Eshel Avraham: 135)!
- According to the Amora Sh'muel, as quoted by R. Yehudah, in Berakhot (21a), the recitation of Sh'ma is merely rabbinic. Accordingly, we could suggest that the enactment to read the Torah on Monday and Thursday preceded the enactment to read the Sh'ma daily. This would be especially likely, since the enactment to read the Torah thrice weekly is very old; perhaps as old as Moshe (cf. Bava Kamma 82a, Hilkhot Tefillah 12:1).
However, some claim that even according to Sh'muel, there is still a Biblical obligation to study Torah each day; just no set formula. (cf. Talmidei Rabbenu Yonah to Rif Berakhot 12b). If that were the case, or if the recitation of Sh'ma were actually Biblical, then another answer would be needed.
- We could suggest that the point of having Torah every three days isn't just that the individual should experience Torah periodically, for which any Torah should suffice, but rather that the Torah itself must be reviewed periodically so that it not be forgotten.
This is implied by the Paneah Razza (14th cent.) who writes (Deut 10:10):
לא יהיו לעולם ג' ימים בלא תורה ולא תשתכח
And that they never go three days without Torah, and it would not be forgotten.
- The P'ri M'gaddim himself gives two answers. Either that one needs to lean Torah besides for Sh'ma (he does not clarify the nature of this need; indeed it seems to be an ad hoc solution). Alternatively, he suggests that there is a need to not exceed three days in Torah study from a written text in particular. (Why there would be such a need, he doesn't say).
- R. Betsalel Stern provides an additional reason (fifth, for anyone counting): that the recitation of Sh'ma does not count as Torah study since it is meant specifically to fulfill its own obligation. (B'tsel HaHokhmah vol. I:1).
[Note that his assumption about the recitation of Sh'ma not fulfilling the obligation of Torah study is dubious. Cf. Nedarim 8a, and Menahot 99b).]