Did you shoot your time lapses with video or pictures? If it is pictures, just put them all in one folder and import the folder. It will come in as a picture sequence. You may have to adjust your import preferences for the duration of each picture. Create a composition and put the picture sequence in there. If you want to speed it up, time stretch it.
I hope that works for you.
If you've shot JPEGs, just work with the sequences (and I'd use "Interpret footage" to change the speed rather than stretching a clip!)
If you've shot RAW, you really want to process the images outside AE. If you want access to all the RAW data you can actually export multiple JPEG sequences with different settings and combine them in AE. Working with RAW images in AE works, but is painfully slow because each frame has to be de-bayered before being shown.
AE has no problems with image sequences. Just import them assign the proper frame rate in the interpret footage settings, or change the default frame rate for image sequences in Preferences.
Import at full resolution, too: you'll then have the luxury of being able to re-compose the shot if necessary, and you can also fake camera moves if you want simply by animating either the layer's anchor point or its position.
Image sequences behave exactly the same in AE or Premiere Pro as video. The determining factor would be the size of the images in an image sequence. If the timelapse was shot as raw images with a 16MP camera then you might want to render them to HD footage unless you need to do some pan and scan to the timelapse.