The Gemora states: Rabbah bar Shila met Eliyahu the Prophet and asked him what HaShem was doing at that moment. Eliyahu responded that HaShem was repeating words of Torah from the mouths of all the sages except for Rabbi Meir because Rabbi Meir had studied Torah from Acheir. Rabbah bar Shila wondered about this, because Rabbi Meir was akin to one who ate the inner part of a pomegranate and discarded the rind. Eliyahu responded that now HaShem was declaring, Meir my son says thus.
The commentators ask: What novelty did Rabbah bar Shila state thtat wasn’t known before? Why did the parable with the pomegranate result in Hashem repeating statements from Rabbi Meir?
The Gemora in Chagigah (27) states: The transgressors of Israel are full of mitzvos like a pomegranate.
A question is posed: Generally, transgressions are considered to be the most offensive kind of sin. Why, then, are transgressors deemed so worthy by the Gemora?
Kollel Iyun Hadaf cites from Rabbi Shimon Maryles, the Yoruslaver Rebbe in Toras Shimon as follows: The Midrash (Bereishis Rabah 84:19) says that after Reuven repented for his sin, Hash-m promised him, "No one has ever sinned before me and repented [like you did]. My son, in reward for introducing Teshuvah to the world, I promise that your descendant will introduce Teshuvah as well." The Midrash identifies that descendant as the prophet Hoshea, who issued a prophecy which begins with the words, "Return o' Israel to Hash-m your G-d!" (Hoshea 14:2).
The Midrash's assertion that Reuven was the first person to do Teshuvah is difficult to understand. The very first man, Adam ha'Rishon, as well as his son, Kayin, engaged in Teshuvah long before Reuven! Apparently, the intention of the Midrash is as follows: Reuven was the first to introduce Teshuvah as a necessary prelude to the performance of a Mitzvah (in his case, returning to rescue Yosef from the pit). The importance of doing Teshuvah prior to performing a Mitzvah is derived from the Tikunei Zohar (Tikun 6), which states that any Mitzvah performed without an adequate blend of "fear and love" of Hash-m does not succeed in rising heavenward, for these two qualities serve as the "wings" of the Mitzvah. This is hinted to in the verse, "They shall raise you up in their palms, lest you knock your foot against a stone" (Tehilim 91:12) -- the "palms" allude to the qualities of fear and love of Hash-m aroused through Teshuvah which protect one's performance of a Mitzvah from the dangers of the Yetzer ha'Ra, often symbolized by a stone.
Thus, when a person performs a Mitzvah it is necessary that other elements be present -- besides the actual execution of the Mitzvah -- in order for the Mitzvah to be credited to that person in Shamayim. Those elements include fear of Hash-m, love of Hash-m, and doing complete Teshuvah before performing the Mitzvah, so that the Mitzvah is performed with the utmost sincerity. When a Mitzvah is performed in that manner, it acquires wings, so to speak, to fly up to Shamayim.
A perpetual transgressor (or "Posh'ei Yisrael") invests none of these elements into the few Mitzvos which he manages to carry out in this world. As a result, his Mitzvos have no means with which to fly heavenward, and instead they settle and accumulate around him, convincing him that he is "full of Mitzvos like a pomegranate." In contrast, the Tzadik -- whose Mitzvos, borne by the thrust of his fear of Hash-m, love of Hash-m, and his Teshuvah, soar immediately heavenward, always appears to himself as bereft of Mitzvos because all of his Mitzvos go straight to Shamayim.
This is also the meaning of the verse (Devarim 30:2), "And you shall return to Hash-m your G-d" -- that is, when you first do Teshuvah, you may "[then] heed His voice" -- proceed with the performance of His Mitzvos, "according to all which I command you this day," so that the Mitzvos can rise heavenward.
This is also the intention of the prayer we recite each morning, "May He place in our hearts love of Him and fear of Him, and [may those two qualities give us the ability] to do His will and serve Him with a perfect heart." It is the love and fear of Hash-m, aroused through Teshuvah, which elevates one's actions.
This idea explains the Mishnah in Avos (4:21-22): "Rebbi Yakov says: This world is like an anteroom before the World to Come; prepare yourself in the anteroom, so that you might enter the banquet hall." The Mishnah continues, "He would also say: Better one hour of Teshuvah and good deeds in this world than the entire life of the World to Come, and better one hour of contentment in the World to Come than all the life of this world." The connection between these two statements of Rebbi Yakov may be explained as follows: How should one prepare himself in the anteroom of this world for the reward of the World to Come? One should prepare himself in this world by doing Teshuvah before every Mitzvah that he does, so that those Mitzvos will rise heavenward on the strength of the fear and love that is aroused through his Teshuvah.
In this sense, it may be said that Rebbi Yakov was actually offering a defense for his grandfather, Elisha ben Avuyah (Kidushin 39b), the Tana who became a heretic and thereafter was referred to as "Acher." The Gemara (Chagigah 15a) attributes Acher's persistence in maintaining his rebellious lifestyle to a voice he once heard echoing from behind the heavenly curtain, which said, "Return, all you wayward children, except for Acher!" One might ask that, granted, the heavenly voice rejected the possibility of Acher repenting for the sins which he had already committed, but what prevented him, in the event that he did feel remorse, from accumulating a new store of Mitzvos that would count in his favor for the future? In answer to this question, Rebbi Yakov offers his insight: "Better one hour of Teshuvah and good deeds in this world than the entire life of the World to Come" -- for without the spiritual advantage of Teshuvah, all of the Mitzvos one does in this world have little effect. This might have been Acher's reasoning which caused him to despair of ever correcting his ways.
Based on this, perhaps we can say that this was the meaning behind Rabbah bar Shila’s statement. Rabbi Meir understood Acher’s flaws but he viewed him as a pomegranate. Acher’s sins were all around him, but Rabbi Meir took the rind from the pomegranate and discarded it, demonstrating that Acher’s mitzvos were worthless and he should not consider himself righteous because of those deeds.