The paragraph
יְהִי רָצון מִלְּפָנֶיךָ ה' אֱלהֵינוּ וֵאלהֵי אֲבותֵינוּ. שֶׁיִּבָּנֶה בֵּית הַמִּקְדָּשׁ בִּמְהֵרָה בְיָמֵינוּ. וְתֵן חֶלְקֵנוּ בְּתורָתֶךָ: וְשָׁם נַעֲבָדְךָ בְּיִרְאָה כִּימֵי עולָם וּכְשָׁנִים קַדְמונִיות:
is found twice during the morning davening -- once after R. Yishmael and once after the amida. The opening idea recalls Pirkei Avot 5 (I have seen it referenced as 5:23, but have found it as 5:24 and 5:20). In the Artscroll siddur, comment is made that the paragraph's appearance after the amida makes sense as the davening replaces the sacrifices. The notes after R. Yishmael point out the same thing as this appears directly after the Korbanot section of prayer (the saying of which is tantamount, in this day and age, to making the offerings, themselves).
In the latter case, there is the addition of Malachi 3:4,
וְעָֽרְבָה֙ לַֽיהוָ֔ה מִנְחַ֥ת יְהוּדָ֖ה וִירֽוּשָׁלִָ֑ם כִּימֵ֣י עוֹלָ֔ם וּכְשָׁנִ֖ים קַדְמֹנִיּֽוֹת
If the two moments serve the same purpose, to recall, and, in a sense, replace the sacrifices, why is the Malachi passage appended to only one of the paragraphs?
[ This source indicates that the entire paragraph was added also to ensure that time passed before people stepped forward, so one could answer that a related verse was added because, over time, people started praying faster so the paragraph was no longer long enough to ensure the proper delay, but I'm hoping for something a little less pragmatic (and cynical).]
