I think The Penguins of Madagascar has improved steadily since the first episodes. While it was always good, episodes like "Operation Plush & Cover" (pretty much a by-the-numbers "Conveyor belt of doom" episode) and "Happy King Julien Day" (which I thought had a very forced twist ending) find the writers shaking out a couple rookie mistakes. Come some of the later episodes, like "Mask of the Raccoon" and "Sting Operation", they start adding interesting one-shots to bring out a little more variety. Then they top off the first season with the intricate "Dr. Blowhole's Revenge", easily one of the best episodes.
Season 2, they seem to be playing to the technological strengths of the penguins even more, coming up with much more creative ideas like "It's About Time", "Lost Treasure of the Golden Squirrel", "The Helmet", etc. The whole tone of the show is a little darker and grittier now, but they still don't shy from entertaining character sketches like "Badger Pride" (also one of my favorites).
Overall, they seem to be relying more on Bill Motz/Bob Roth, Eddie Guzelian and Brandon Sawyer the most. Sawyer did some of the "darker" episodes in late season 1, Motz and Roth are good at everything they do, and both they and Guzelian seem to have the best handle on the show's characterization and tone.