Ok so with the knowledge that there are going to be a second and third Avengers films here is what I would do if I were Joss Whedon. First of all Thanos, who was revealed to be a future threat for the Avengers in the first film, should be saved for the last film of the series and here is why:
The first film had Loki as the main villain which is not really a threat to the Avengers which is why the Chitauri and the Tesseract were needed. However, Loki is a villain that Thor can defeat on his own as is usually the case in most Thor comics and in the movie. Therefore the villain for the second film should be a threat that an individual that an individual cannot face alone. I'm thinking of someone like Ultron or Kang or the Masters of Evil for the next film mainly cause that would be the only way to top the threat of Loki in the first film. Thanos should be saved for the last film because he is the biggest threat not just to Earth but to the entire universe and therefore the grand finale should be the most epic conflict in the Marvel Cinematic Universe and if I had any say I would not include just the Avengers but everyone in the Marvel Cinematic Universe including the Guardians of the Galaxy, X-men, Spiderman, etc. would be involved.
Also the scope of the battle needs to slowly increase until the grande finale in the third film which would span the galaxy or the universe. But with the final battle of the first Avengers film only being set in New York then Avengers 2 should involve all the earth. For example, Ultron could unleash an army of robots on capital cities of the world, or Kang could unleash his army in just the same way. If the Masters of Evil are the villains then each individual member could lead an army to assault different cities of the world such as Baron Zemo leading an assault on Berlin, the Leader could lead an army of gamma monsters into Washington DC, Enchantress could lead an amy of frost giants, Crimson Dynamo could lead an army of humans in Iron-Man like armor, etc.