Recently, I was checking Obfuscation techniques in Android for one of my courses. I found out an academic repository on GitHub named Obfuscapk which is for obfuscating Android APKs. This is the paper of their work which you can study if you like.
I have collected the using of the tool in a video in my YouTube Channel. I publish my videos over there, so you can view them. About the Obfuscapk, there is a critical point of using one obfuscator per step. I mean if you want use 5 obfuscator, you should the obfuscator 5 times (one in each step). And using the three plugins with the shown order is critical (Build => New Signature => New Alignment)
I have tested the obfuscator on famous 2048 puzzle game which I was another post about Smali code injection on the same app.
But the video about the Obfuscapk is here: