In some ways they did but you've gotta respect the main-series games.
The Pokemon and character designs, the basics of the game, the battle mechanics, even the very idea comes from the original.
But all Pokemon games have their own ups and downs, even the so called 'bad' ones.
Come the think of it we wouldn't even be here discussing this if not for a certain fan-game, the fact that someones dedication and love for the franchise brought us here together is amazing and something I would love to see develop in the future.
Overall I think fan-games and main-series games complement each other and co-exist just fine.