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The Rema brings a minhag to put grass and other herbage in shul for Shavuos. I've seen this practiced only once. Why don't more Ashkenazi shuls follow this minhag?
I feel some would be tempted to say that the Gra annulled this minhag, as brought in that Simman by the Mishnah Berurah. But if you look carefully, he's discussing a different minhag: to put trees in shul. That minhag was brought by the Magen Avraham, not the Rema.
While your thought, that the Vilna Gaon only prohibited trees, has become popular recently with the popularization of Christmas trees, it's not historically accurate. He prohibited greenery on Shavuot because it paralleled the greenery set up in churches (especially Orthodox ones) for Pentecost (the Christian holiday which parallels Shavuot) which commonly includes birch branches and red flowers. This is noted explicitly in his student's Chayei Adam (131:13):
והגר״א ביטל מנהג מלהעמיד אילנות בעצרת משום שעכשיו הוא חק העמים להעמיד .אילנות בחג שלהם שקורין זאלאני״ע או פינגסט״ן
And the GR"A nullified the custom to put up trees on Shavuot because now it's the practice of the nations to put up trees on their holiday that they call Zelelnia or Pfingsten.
That's all the Chayei Adam wrote. He never mentioned a custom about "grasses" beforehand that you can learn that he meant "trees" specifically and not "greenery", nor would such a read make sense since churches on Pentecost don't exclusively use trees. Indeed another of the Vilna Gaon's students, R' Mordechai ben Aryeh Leib, wrote (Sefer HaLikuttim):
מנהגו של החסיד שביטל העשבים בשבועות אף שהרמ״א הביאו...
The custom of [the Vilna Gaon] who nullified the grasses on Shavuot even though the Rama brought it.
Igrot Moshe (YD 4:11:5) also understands the Chayei Adam and Vilna Gaon to be referring to both "trees" and "grasses" because of Pentecost.
The Arukh haShulchan, after writing about the old customs of both "grasses" and "trees", concludes:
אמנם בדורות שלפנינו ביטלו האילנות והעשבים, מטעמים שידעו הגדולים שבדור.
However, in the generations that preceded us they nullified the [customs of] trees and grasses [because of the Vilna Gaon].
The Arukh haShulchan's assessment of common practice matches yours.
(I note though the custom is still alive and well in some communities.)
