The 5-2 victory at the Madejski Stadium lifted a bit of the pressure from manager Arsene Wenger's shoulders following their shock Capital One Cup defeat by Bradford but there remains plenty of speculation about his future.
The Gunners head to Wigan on Saturday only two points outside the top four but closer to the relegation zone than they are to leaders Manchester United.
But Latics boss Martinez said: "I don't understand it from the outside.
"You look at this Arsenal side, they've had to cope with many players moving away and new players coming in. They need a little bit of time but I went to see them on Monday and they were very impressive.
"I thought the movement and the quality of play they had in possession was as good as I've seen from an Arsenal side. Players like Lukas Podolski and Santi Cazorla, they're starting to feel themselves in this league.
"This Arsenal side will never change the way they want to win football games, the football philosophy that they've got, and that's admirable.
"You're going to see this Arsenal side going from strength to strength. They're still in the Champions League, which is the best competition in the world, and I think this team has got a lot to offer."
Martinez and Wenger share a very similar philosophy based on possession football, and the Frenchman has largely come out on top in his battles with Wigan.
Arsenal have won 10 of their 14 Premier League meetings but the Latics have certainly had their moments, including beating Arsenal to reach the Carling Cup final in 2006 and famously coming back from 2-0 down to win in the league in April 2010.
Last season brought another notable success as Wigan triumphed 2-1 at the Emirates Stadium - their first victory at the home of Arsenal and a crucial three points in their successful fight against relegation.
"Our games against Arsenal are two teams with similar football concepts," said Martinez.
"We both battle to have control of the football and the games are really open, there are chances. They're really exciting to watch, especially from a neutral's point of view.
"We had a great moment in 2010, to be able to come back from 2-0 down, you don't get that opportunity against Arsenal too many times and it meant a lot that season, it allowed us to achieve our aim.
"Last season going to the Emirates and being able to get our first ever win at Arsenal was a key moment in our season in terms of belief and assurance that we could achieve our aim and Saturday is going to be another incredible event - the last game in 2012 at the DW Stadium.
"It's been a fantastic year of football at Wigan Athletic and we hope we can give something to the fans to fit the occasion."
Wigan are once again in need of three points after picking up only one from their previous four games - a run that has seen them drop into the relegation zone.
Injuries are taking their toll, and Martinez could be without eight players tomorrow.
Four will definitely be missing after defender Adrian Lopez (hamstring) joined midfielders Ben Watson (broken leg), Ryo Miyaichi (ankle) and Albert Crusat (knee) on the long-term injury list.
Another four players should feature over the festive period, with captain Gary Caldwell (hamstring) the most likely to make it for Arsenal ahead of fellow centre-backs Ivan Ramis (hamstring), Antolin Alcaraz (groin) and midfielder James McCarthy (ankle).
Reinforcements are on the horizon, though, with midfielder Roger Espinoza receiving clearance from the Football Association this week to join from Sporting Kansas City in January.
And Wigan are also reportedly close to completing a loan deal for 18-year-old Manchester United and Chile forward Angelo Henriquez.
United's Tom Cleverley benefited from a loan spell with the Latics last season, and Martinez said in the Daily Mirror: "Angelo is as good a goalscorer as you will find.
"He scored goals at Universidad de Chile and he is going to score goals here. I am sure he will be an important player for United. We are glad we can work with him and he can use Wigan as Tom Cleverley did and adapt to what is needed in this league."