Diego Simeone's side did upset Real Madrid in the final of the Copa del Rey, however, with a 2-1 win at the Bernabeu enough to secure the trophy.
Atletico have started the 2013-14 campaign in fine fashion, with many suggesting that they could break up the dominant two in Spain this season.
With that in mind, Sports Mole offers its opinion on whether third is the best that the capital outfit can hope for come May 2014.
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Simeone, at least publicly, does not believe that that his side can mount a serious challenge for the title this season, with the Argentine recently claiming that La Liga is "a boring championship" due to the dominance of Barcelona and Real Madrid.
In the last four seasons, an average of 21 points has separated second place from third, which aids suggestions that the gulf between the leading two teams and the rest of the division is a gap that cannot be overcome.
Barcelona have won the title six times in the last nine seasons, with Madrid claiming three successes during that period. The last time that a team outside of the top two secured the crown was in 2004, when Valencia, who had also picked up the title in the 2001-02 campaign, were victorious.
The fact that this discussion is even taking place when Atletico sold Radamel Falcao, their best player and top scorer from the last two seasons, to Monaco this summer is credit to the team that Simeone has put together. They are not the most pleasing on the eye at times, but the experienced Argentine has assembled a squad of players that know what it takes to operate at the highest level.
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They have started this season in spectacular fashion, with a 3-1 win over Sevilla at the Estadio Ramon followed by an emphatic 5-0 victory over Rayo Vallecano at the Vicente Calderon on Sunday.
They also managed to pick up arguably the signing of the summer when David Villa was allowed to join from Barcelona for a figure in the region of £3m, which in the current climate, gets more extraordinary with each passing day. Simeone needed a big name to appease supporters after allowing Falcao to seek pastures new and the 43-year-old managed to do just that.
Atletico travelled to Real Madrid and Barcelona in December of last season, but despite entering the match in a fantastic run of form, they were comfortably beaten 2-0 by their capital rivals before losing 4-1 to Barcelona at the Camp Nou.
It was a similar story when Simeone's side welcomed the pair to the Vicente Calderon, with Real Madrid leaving with all three points at the end of April, before Barcelona claimed a 2-1 win in Atletico's penultimate match of the league season. They were undoubtedly impressive last year, but still came up short against the best two teams in the league.
Not too much should be drawn from their 1-1 draw in the Spanish Super Cup first leg against Barcelona last Wednesday, but it is difficult to overlook what they achieved against the league champions. In the first half, Atletico utterly stifled their opponents and although Barcelona found a goal in the second period, there was something different about the result. For the first time in however many years, Atletico looked on a level playing field.
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Atletico do not have a Lionel Messi or a Cristiano Ronaldo in their team, but what they do have is a first XI which can stand alongside the major teams in European football. On paper, injuries permitting, their strongest side would read: Courtois; Juanfran, Godin, Miranda, Luis; Gabi, Suarez, Koke; Turan, Costa, Villa.
Ah Diego Costa... the Brazilian who was the subject of a £20m bid from Liverpool this summer. The fact that the powers-that-be at Atletico quickly dismissed that bid before handing the forward a new contract tells you everything that you need to know. He scored 10 goals in the league last season, but has already hit the back of the net three times this term.
In Thibaut Courtois, they have, on loan at least, one of the best young goalkeepers in world football. Their defence kept 20 clean sheets in the league last season, with their record of just 31 goals conceded quite comfortably the best in the division. There are not too many better centre-backs than Diego Godin, whose partnership with Miranda has flourished in recent seasons.
Taking a look at Barcelona's current defensive centre-back pairing – Gerard Pique and Javier Mascherano – and Madrid's – Pepe and Sergio Ramos (with Raphael Varane still on the sidelines), it is difficult to argue that the current top two are better equipped in defence.
In midfield they also possess the experience and guile of Gabi, whose talents bring out the best in Koke, who has managed to work his way into the Spanish midfield. That is without mentioning the powerful Mario Suarez, who has developed into one of the finest players in his position under the stewardship of Simeone – who was a decent midfielder in his day so I hear.
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When you scratch the surface, they also have the likes of Tiago Mendes, Cristian Rodriguez, Leo Baptistao, Martin Demichelis and Adrian Lopez – players that would walk into any team in the league apart from the top two. A special mention must also be given to Oliver Torres, who is without question, one of the best young talents in world football. If you haven't seen too much of the 18-year-old, then be sure to remember his name.
Without opening up a can of worms, the problem that Atletico face is the well-documented financial problems in La Liga, with the television rights which present Barcelona and Real Madrid with an utterly comprehensive percentage of the money leaving the remaining 18 clubs to battle the crisis that is occurring in Spanish football.
The likes of Roberto Soldado, Jesus Navas and Alvaro Negredo decided to move to the Premier League this summer, which has posed the question - where is La Liga going? Will we get to a stage where the top two in Spain rack up rugby scores at half-time with the two powerhouses in European football breaking the 100-point mark each season?
In truth, it is difficult to imagine Atletico finishing higher than third this season. But that isn't to say that Simeone has not put together a side that is moving closer to the leading two teams in Spanish football. The problem this season will be whether they can balance European commitments with those closer to home, but it is a situation that Simeone will relish.
Atletico picked up 76 points last season, a total that would have left them two points shy of second-place Manchester City in the Premier League. I have no doubt that can better that tally this time around, but with Barcelona and Real Madrid both threatening to surpass 100 points and with both still in the market for new players, Atletico will once more have to settle for third despite their incredible progress over the last few seasons.