It was always a political game. Poland used to have some unresolved issues with Lithuania (like the status of polish minority there). Lack of good train connections and highways was used as a way of pressure by Polish government on Lithuanians.
From the economical point of view, do not expect a high-speed passenger train. Eastern Poland and Baltics are not so dense populated to justify such a big investment.
Honestly speaking, I wish an old 19th-century, shortest connection Warsaw - Hrodno - Vilnus could be reactivated. But as long as it crosses Belarus (which is not a EU member) this seems impossible.