I guess they wanted this Four Sword continuity to have the same graphical style. 'sides, all three Gameboy games had the same graphics. (Link's Awakening, Seasons/Ages).
Personally, I have nothing against the train idea. It's not a big change probably. Every Zelda game has a 'thing'. Boat, Changing weather, time travel, bird summoning, 3 shadows, mini cap, wolf form, wind changing... now a train. Whatever! It'll still be Zelda fun.