Assuming they are both in the same condition, it is logical to consider upgrading the L28 instead of the L26. Either one will fit into any 1st gen Z. You will find more aftermarket and NISMO modifications for the L28. Since it is further refinement of the Nissan L6 block, it has subtle improvements and is more reliable than previous versions. It is not only bigger than previous blocks -- it is better.
Many parts and accessories are interchangable.
But if the L26 is running fine, there are a lot of things you could do to it that could be re-used in a future L28 rebuild. A new cam, headers, maybe cyl head work, carbs, fuel delivery, starter, cooling, etc etc etc.