One ubiquitous and ancient feature of Indo-European languages is a lack of contrast between the nominative and accusative for neuter nouns.
I'll restrict attention to nouns here and not independent pronouns.
This old question asks why the neuter nominative-accusative merger happened, but I'm interested in a slightly different question: namely, whether any languages have undone this merger through subsequent innovations.
This answer mentions an ergative-like suffix -ants that marks neuter nouns in Anatolian languages.
Innovating an ergative case for neuter nouns, though, is not exactly the same thing as creating/restoring a nominative-accusative contrast in neuter nouns, but it does result in a distinction between two core neuter arguments in transitive clauses, so it counts to some degree.
I'm primarily interested in cases where the neuter has been retained and a way of distinguishing neuter core arguments in transitive clauses has been innovated through the introduction of a new case. Merging, say, datives and accusatives across the board would also count. I would say that removing the neuter gender entirely does not count. A hypothetical Romanian-style merger, where the neuter behaves like the masculine in the singular and the feminine in the plural, that happened to distinguish nominative and accusative would also count as a borderline case.