In the Japanese version of the game, you can skip through the title screen and main menu by holding Start when resetting or booting up the game. In the western version, it's no longer possible to skip through the title screen and main menu.
In the Japanese version of the game, the Rapier, Reginleif, and unused Mani Katti are the only anti-cavalry weapons that don't receive an effective bonus against Mage Knights, Tarvoses, and Maelduins. This was fixed in the western version.
Several characters had their base stats and/or growth rates tinkered with when the game was localized in the West. Lyon's in particular were greatly improved (he had lots of 10% growths before).
Many weapons were altered when the game was localized in the West, such as the lowering of Siegmunde's Might (19 to 17), and the raising of the Brave Axe's worth (2250 to 7500).
In the western version of the game, many shops had their stock and/or the order of their stock changed visited during a chapter. Most notably, the western version allows players to purchase the Nosferatu tome in the Chapter 17 shop, while it can't be purchased in the Japanese version. On the flip side, the western version doesn't allow players to buy stat-boosting items from the Secret Shops during the storyline.