- batch process your images to save system resources
- create a dynamic link between Premiere and After Effects
- create a camera and null object within After Effects to apply to your time-lapse
- create a pan (or zoom) in your time-lapse
See also Creating Timelapse Movies in After Effects, with an example by Ross Chang and a similar tutorial from Rich Harrington. [update: targeted more to Photoshop users is QuickHit #8: Creating Time-Lapse Movies in AE (Pt. 1) from Colortrails.]
By the way, After Effects has a filter called Color Stabilizer to fix flicker in time-lapse (see also the "auto effects"). Granite Bay has a nice guide on causes and cures to fix it, and a video on using their AE plug-in GBDeflicker. There's also GenArts Tinder DeFlicker which has about six ways to remove flicker to do multiple passes, but there's no CS5 version yet.