The reason for the fillers is because the animation team needs time to develop the plot related episodes. If I remember correctly, the animation team is around 4~ months ahead of what's being shown on TV. Maybe even farther than that!
The reason why BW was so bad, as an example, is because they simply did not plan on the earthquake ruining the plot they had in mind for BW, and didn't know how to recuperate for lost time. This is a team that's direction is literally "Advertise the hell out of the games, and you will generate All The Money". And sometimes, they may need to use filler, to continue to buy more time to make plot stuff. SURE, I would love if the anime had plot out the wazoo, but admittedly, the anime team isn't SUPER full of effort, and in fact, can be kinda lazy with episode ideas. Such as reusing episodes in the past, and justifying it as "Kids don't know those episodes!".
Maybe these fillers could have, AT LEAST, new moves for Pokemon, or even someone becoming more important down the line...? The anime is weird, yo.