There is minor trainer customization (appearance and starting town) and you can tackle all 16 gyms in any order. Gym leaders' levels and team compositions will scale up based on the number of badges you have. After you've conquered them all, you can re-battle them at whatever 'badge scale' you wish, to take on their strongest or weakest teams. You need a total of 8 badges (any 8) to challenge the Elite Four.
Version 2.5.5
All 251 Pokemon made obtainable
7 different male and female trainer sprites to choose from, with basic color customization
28 different selectable starter Pokemon
Restoration of Kanto dungeons (Safari Zone, Cerulean Cave, Seafoam Islands, etc.)
Following-Pokemon, and unique menu sprites for each Pokemon species
Running shoes, and fast-travel options
Dedicated NPC for trade-back evolution