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Version comparisons
Title screen
The title screens are different between both versions. The Mega Drive version features a static image depicting a 3D model of Pikachu, while the SNES version features an animated 2D pixel graphic of Pikachu (and also mispells Arcade Mode as "Arcade Moe").
Pokémon select
A different background is used for the Pokémon select screen. The roster also features different Pokémon.
The VS screen displayed after selecting Pokémon has an animated background in the Mega Drive version, whereas the SNES version has rotating palettes.
Battle
The Mega Drive version begins a battle with an animation of a Poké Ball being thrown. The SNES version simply has a mosaic transition to the battle.
The HUD is different between both versions, with the Mega Drive version taking advantage of a higher horizontal resolution.
Skill selection is displayed at all times in the Mega Drive version, though skill names are not displayed when making a selection - only when the skill is used.
The SNES version displays defensive commands as icons with descriptions when highlighted. The Mega Drive version only uses a text-based menu.
References
