Hyperdimension Neptunia Re;Birth 1 is easily my favourite updated re-release of a game, it takes the fantastic dialogue from the first game and gives it Victory's battle system, which is substantially better than the gameplay of the original title, which was slow and clunky and vastly inferior to Trinity Universe, which was out around the same time. Re;Birth 1 is what we should have gotten on PS3 in the first place.
Honorable mentions go to Pokemon HeartGold/SoulSilver, for being the last Pokemon titles to capture the magic of my childhood; Disgaea 4: A Promise Revisited, for adding in all the DLC and then some and incorporating the only good idea D2 had (the Cheat Shop); The Legend of Zelda: The Wind Waker HD, for making sailing much faster and thereby removing 90% of the tedium from the game, making it so much better for it, and Final Fantasy Tactics: The War of the Lions on PSP, for being the best Final Fantasy title to date. There are others, but those are the ones that immediately sprang to mind.
Speaking of, I expect and demand a Final Fantasy XII HD remaster or a PS4 port to take the top spot by the end of the year, though. Make it happen, Square Enix. MAKE IT HAPPEN. The best mothership title deserves at least a PS4 port, if not a full-blown HD remaster of the international version.
Atelier Rorona Plus gets a mention for best improved re-release, as well. The quality of the original Rorona left a lot to be desired, the overhaul the Plus version gave it was far more noticeable than any of the other titles Plus re-releases; it was like a brand new game altogether.
I love the opportunity to revisit my old favourites, whether it be as ports or remakes or remasters. I just wish people would learn the difference between the three terms and apply it properly, instead of just labelling everything as a remake.