The best replacement for multiwii is apm.

The best alternatives to multiwii are rated as following:
★★★★★  apm
★★★★★  megapirate
★★★★  kk2
★★★★  naza
★★★★  arducopter
★★★  kk2.1
★★★  kk2.0
★★★  openpilot
★★  kk
★★  megapirate ng
★★  ardupilot
★★  aeroquad
★  cc3d
★  naze32
★  apm 2.5

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Google Trends

Scale is based on the average worldwide traffic of multiwii in all years. Click on graph for more.
multiwii
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