The best replacement for barium enema is colonoscopy.

The best alternatives to barium enema are rated as following:
★★★★★  colonoscopy
★★★★  ct scan
★★★★  barium swallow
★★★  virtual colonoscopy
★★★  gastrografin
★★  sigmoidoscopy
★★  barium meal
★  ct colonoscopy
★  ct colonography
  follow through
  gastrografin enema

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Speaking about barium enema, one probably shouldn't forget about intussusception.

Other search terms related to barium enema and their ratings are:
★★★★★ intussusception
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barium enema
colonoscopy
ct scan