New Features

Features intentionally added to the games themselves, beyond what the original cartridges shipped with:

Survey zoom with connected-map rendering and configurable void fill
Perspective tilt mode for an HD-2D-style overworld
Multiple color modes, including original, SGB, advanced GBC, monochrome, and classic green
Optional GBC screen effects, including pixel grids, shadows, glare, and transparency
Performance presets and configurable FPS limits
V-SYNC row and a DISPLAY frame cap, for panels whose refresh is not a multiple of 60Hz
LOGIC CLOCK option (60HZ or the cart's 59.73HZ vblank rate) on every game's options screen
Peer-to-peer LAN link play for trades and battles between Red, Blue, and Yellow
FireRed/LeafGreen online over the relay (Union Room, Direct Corner, wireless minigames, PIN-locked private matches, in-game invites)
FireRed/LeafGreen Mystery Gift on the main menu after the first save: WONDER NEWS right away, WONDER CARDS once the questionnaire passphrase is in
Optional widescreen battle layout
Pokédex diploma and printer image exports
Fast-forward locks to 1X in link play, every link or online battle, link session and the FireRed/LeafGreen Union Room on every game
40-player Union Room on FireRed and LeafGreen online, a larger square room where every trainer keeps a fixed spot and anyone can be talked to

Gen 2 Specifics

Battle screen options on Gold, Silver and Crystal: BATTLE SIZE (fixed or window-filling) and BATTLE BG (white, black or the dimmed map as the surround)
Widescreen battle layout on Gold, Silver and Crystal: BATTLE LAYOUT -> WIDE spreads the HUDs and bottom windows across a 304-wide screen
Extended battle HUD on Gold, Silver and Crystal: BATTLE HUD -> EXTENDED docks the WIDE layout's foe panel to the top of the window and the text area and player panel to the bottom
Event tickets on Emerald: OPTION -> EXTRAS -> EVENT TICKETS lets the Lilycove Mystery Gift man hand out the Eon, Aurora and Mystic tickets and the Old Sea Map