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Is your .mt2s files from Blu-ray? Do you have original BD? If so, you can rip BD into iPad friendly format directly with a professional tool.
Brorsoft Video Converter for Mac can help you encode one audio file into another audio file. Have a try! It not only can deal with audio files, but also can help users to encode common video files for playing and editing.
As we all know, the most compatible video format for Adobe Premiere and Avid editing is MPEG and DNxHD MOV format. So we need to transcode the Blu-rays to the editable format first before import the Blu-rays to the editors. In order to perform the task smoothly, I recommend you a powerful Brorsoft Blu-ray Ripper for Mac which has an exclusive function to support Blu-rays and DVDs to editing tools, such as Adobe, Avid even FCP.
After Effects announced on their official website long time ago that it could support AVI videos without problem. But the fact is that some AVI videos are rejected by it. As far as we know, AVI is a 'container' which can incorporate most any sort of video and audio format. That is to say, AVI videos can be encoded by different codecs like DivX/Xvid, which makes After Effects refuse them. Then how can we make all AVI files compatible with After Effects? The best workaround is to encode AVI to MPEG/MOV(AVC)
I found an article online, which may be helpful to you.
I used a tool which is recommended by some professional forums. It is much professional on dealing with DVD/BDs. You can have a try.