AE cannot handle anything with more than 99 FPS, so yes, the framerate is the problem plus of course AE is picky with those atrocious free CoDecs. Doesn't make much sense, anyway. AE will use your TGA sequence just the same.
Okay, to clear things up. I recorded with 2000 Fps to obviously have enough frames to make a smooth slow motion.
So you say, I can import my .tga-sequence into after effects. When I do so, by default it wil set the sequences frame rate to the comps frame rate. But i want the sequence to playback in original speed and if I understand you right, I can't say after effects to treat the sequence as an 2000 fps footage? :/
Btw: before I recorded in 2000 fps, I made a little test with 120 fps. And After Effects did import that.
The frame rate is not a problem at all if you do some math. I work with high frame rate footage all the time. If you shoot 2000 frames per second it is usually for the purpose of slowing things down in playback. The error message you are getting says that the format is unsupported so you need to transcode the footage. Transcoding will not change the frame rate, but you'll not have much luck playing it back in real time. Once transcoded, or even rendered to an image sequence you can import it into AE. The frame rate of video files is just metadata, it has nothing to do with the actual frames except that it will try and tell the media player how many frames per second to try and use for playback.
Here's your workflow. Say you want your 2000 fps footage to turn 1 second of real time into 1 minute of real time. You simply divide 2000 by 60 and get 33 (rounded off) frames per second. You import your footage into AE and interpret it as 33 frames per second. Now you want a portion of that footage to play at real time then slow down, then return to real time. Simply enable time remapping on the layer. set a keyframe where you want the footage to slow down and then another where you want the footage to speed up. To get your footage to real time you do math again. 1 minute of playback is 1 second of real time so you place a marker at 1 second, then with the last 3 keyframes selected and the CTI set at the one second mark you drag the keyframes toward the CTI with the shift key held down and snap the first of the selected keyframes to the CTI. The footage now plays back in real time for the first second, then changes to slow motion. To get the footage to go back to real time you simply grab the last keyframe and move it closer to the third one. I hope that's clear. Of course none of that will work until you convert your original footage into a format that AE supports.