Not only was it that they were buried in Gondor, but their bodies would be laid to rest next to Aragorn's...truly a mighty honor for any halfling. I think however, it's just the fact that Merry and Pippin both decided to go to Gondor and spend the rest of their life their:
Quote:
It was heard after that Master Meriadoc came to Edoras and was with King Eomer before he died that autumn. Then he and Thain Peregring went to Gondor and passed what short years were left to them in that realm, until they died and were laid in Rath Dinen among the Great of Gondor.
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Then we find out when Aragorn dies Merry and Pippin are placed beside him.
I mean sure I think Merry and Pippin loved the Shire, but they were on this journey for I believe over a year and growing in friendship with everyone in the Fellowship, so it was only "right" that they were set beside Aragorn when he died. First it being a great honor to any halfling, but also showing the friendship all shared during life.