The best replacement for flixel is flashpunk.

The best alternatives to flixel are rated as following:
★★★★★  flashpunk
★★★★  starling
★★★  haxeflixel
★★★  cinemagram
★★  stencyl
★  love2d
★  citrus

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

Other search terms related to flixel and their ratings are:
★★★★★ flashdevelop
You have in mind a companion for flixel and it is not yet here? Propose!



Google Trends

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