There's a famous story related to Honoring one's parents (Seder Hadorot 3, [here]) about R' Yehoshua Ben Elem that was shown (from above) that he's sharing a place in Olam Habah with a simple butcher.
When I was in the Ohr Sameach Yeshiva I asked a Rabbi, the whole current Torah World is built around producing Talmidei Chachamim as R' Yehshua, but nobody's trying to educate such butchers. I did not receive an answer.
You are absolutely right, noticing, that the Torah does not order the Mitzvot by value (as in Avot "אי אתה יודע שכרן של מצוות") and the Sages usually only emphasize a single Mitzva (Shabbat, studying, Gma"H, and same for negative Mitzvot - mkurder, idolatry, Z"l etc) instead of building a clear hierarchy. This was a real mystery for me until I met my Rabbi some 10 years later. Now I know two ways to resolve this contradiction:
1. Litvakes vs Chassidishers approach
The difference in the two approaches comes from what Rashi (based on ויק"ר ל"ו) brings on the first word in the Torah "בשביל תורה שנקראת ראשית ובשביל ישראל שנקראו ראשית". Those are the two complementary purposes of this world - one is the goal of learning the Torah and the second of "becoming a good Jew" so to speak. Traditionally, despite of many rabbinical stories, the first approach took precedence, implying that studying Torah will ultimately lead to the second goal also. This is the Litvakes approach, currently de-facto standard of the Orthodox Judaism. Important to note, that the highest rank here would be a Gaon, that know all the Torah by heart.
The Chassidishers approach is based on the Mishna in Berachot (5, 1) "חסידים הראשונים היו שוהין שעה אחת", so the Gemorah asks about spending 9 hours a day in prayers - and it seems to be fine with this way of serving Hashem. Indeed, the Chassidut (based on the Talmud and then AriZ"l and then Baash"t) sees any Mitzvah being properly intended and fulfilled as a legitimate way of connecting to Hashem. The purpose of this approach is to turn oneself from physical to spiritual, and therefore, the highest rank here is Kadosh.
To sum it up: according to Litvakes, Torah study is the ultimate time-spending, according to Chassidim - any Mitzva (especial physical ones) with proper intention is as good as studying the Torah.
NB: Please notice, that the current Chassidim, especially in Israel are greatly influenced by the Litvakes!
2. Ariz"l's approach (not necessary, sources needed)
I can't pinpoint where he brings it, but he speaks about everyone fulfilling his own goal as set by Hashem. We can learn it from "יש הקונה את עולמו בשעה אחת" (see Avodah Zara 17 on) - some people reached their high by performing only one Mitzvah, being the essence of their life. Tsis approach is very problematic as nobody is revealed his purpose in life. Many Poskim discussed this point (sources needed) offering some guidelines, for example overcoming the most difficult personal behavior (based on "לפום צערא אגרא") or the opposite - following own best personal traits.
According to this approach, we can choose certain Mitzvot to excel in, based on personal preferences, be it studying Torah, Gma"H, prayers, Maaser or withholding from overriding ones.