Here is the standard methodology when using IDA Pro for Android APK analysis.
You will rarely find a clean, un-obfuscated library. Here is what professionals do. ida pro android apk
The Android open-source community uses the Obfuscator-LLVM to flatten control flow. Code becomes a giant switch-case. Use the Hex-Rays Decompiler and look for the variable that controls the state machine. Patience and scripting (IDAPython) are required. Here is the standard methodology when using IDA
If your goal is to reverse engineer an entire APK (not just native libraries), IDA Pro is overkill and misaligned. Here is the correct toolkit for each layer: ida pro android apk