The best replacement for m2ts is mkv.

The best alternatives to m2ts are rated as following:
★★★★★  mkv
★★★★  ts
★★★★  mts
★★  h.264
★★  avchd
★  vob
★  m2t
★  mpls
  mp4 hauppauge
  m4v
  mt2s
  mts file

Your alternative for m2ts is not listed? Suggest!
Speaking about m2ts, one probably shouldn't forget about tsmuxer.

Other search terms related to m2ts and their ratings are:
★★★★★ tsmuxer
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m2ts
mkv
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