1. The Vilna Gaon famously states that Chazal always had multiple reasons for a Minhag, some of which they may have had some reason for concealing from us, and that therefore we may not unilaterally determine that a Minhag is no longer applicable. Obviously, this would only apply to Minhagim that are certified by Chazal. [As I have had to point out to skeptics many times, this is not at all far-fetched; both as a parent and as an educator I do this all the time.]
2. In the specific case of Yom Tov Sheini, Rav Hirsch explains at length that this Minhag preserves for us the true character of our Yamim Tovim, which would be lost if we were to observe only one day of Yom Tov. Check his commentary to Parashas HaChodesh [Shemos 12].
3. We should not be so arrogant as to assume that we fully understand the basis for a Minhag without extensive research, much less should we assume the authority to revoke a Minhag as obsolete. There are many stories of Rabonim who declared certain Minhagim to be Minhag Shtus, only to learn the hard way why they were wrong, corroborating this idea. [One excellent example, which I think has already been mentioned in the CR, involves the Rema and the Minhag in Cracow to say Mazal Tov after leil tevila.]