Barca and Madrid have occupied the top two positions in La Liga for the last five seasons, with the last league winner outside the dominant pair coming in the 2003-04 season when Rafa Benitez led Valencia to glory.
Filipe, who joined Atletico from Deportivo La Coruna in 2010, feels the duopoly over the title race makes La Liga boring to watch at times and is frustrated at the huge imbalance in funds available to the top clubs.
"We are talking about two teams that no-one can compare to," the Brazilian left-back told AS.
"It is a tremendous injustice that the league is so unbalanced. That Barca and Madrid have budgets that are so immensely greater increases doubts that this is the best league in the world.
"It is more interesting lower down in the table than it is in the fight for the title.
"[At Atletico] we have to try to fight with our weapons. We, with much work and humility, have barely reached them.
"From humility we have achieved many things, but to fight them is very complicated."
The 28-year-old is still positive about Atletico's current side, however, and believes they can continue to make their mark domestically and in the Champions League after lifting the Copa del Rey last term.
"The team is in a great moment. The fact that most of the team is the same as three years ago helps. Almost all the other teams have been dismantled and lost many players and we have not," he said.
"We have maintained our core. [Radamel] Falcao was the great reference for last season but now we have David Villa, who will give us a lot.
"The team is playing the same way as two years ago. We have had many training sessions and years together.
"It shows that we are familiar and that we have not changed much from year to year."
