Personally I would say: “the issue with v2 is its design, not its implementation” or “one of the issues with v2 is its design, not its implementation”. However

Personally I would say: “the issue with v2 is its design, not its implementation” or “one of the issues with v2 is its design, not its implementation”. However your initial phrasing is perfectly intelligible, and probably grammatical (not that that’s so important, if it’s intelligible).