Pros:
1) The speed - Brilliant minds can think fast and accurate. The Manhattan Project crew had a tight deadline. Both of these aspects are beautifully tied into the story-telling through the rapid-fire type short and quick scenes.
2) Non-linearity: This is standard Nolan, and well-done again. Mixing up color and b&w shots is very artful.
3) Strong Cast: Downey JR is the best, closely followed by Murphy.
4) Philosophy: Standard Nolan, this time about fate of the real world.
Cons:
1) Sounds: Overdone, loud sounds, sometimes killing the mood rather helping build it. Rarely is it just perfect, Nolan kind of botched this one.
2) Focus: Story shifted focus near the end, lost momentum.