I've used after effects for a while and intergrating it into your art style can be one of the biggest issues. Say I create an effect that stylizes my fire in each animated frame. ( Hand drawn texture style fire) Once i've imported this into my game , its almost like the rest of the game has to be doped with similar effects that can give a displeasing result.
Help us scope out what you are planning to do:
What's your experience with After Effects
What special fx are you planning to do ?
Think about the visual continuity of your effect.
If you plan to simply follow a after effects guide for an effect and believe it will fit seamlessly into your production. I'd say steer clear of after effects. Generally a solid understanding of colour and visual style will help so if you've got some experience post some pictures of the concept you'd like to achieve.