IOS – Songs in the library “cannot be played on this iphone” anymore

You can use X Lossless Decoder(XLD) too:

X Lossless Decoder(XLD) is a tool for Mac OS X that is able to decode/convert/play various 'lossless' audio files. The supported audio files can be split into some tracks with cue sheet when decoding. It works on Mac OS X 10.4 and later.

because it's lossless it keeps the best sound quality.

Apple recommends using the following formats for your iTunes:

• Audio files (AAC, MP3) with appropriate file extensions (.m4a, .mp3). For best results during playback, Apple recommends converting MP3 files greater than 32 megabytes (MB) to AAC format. For AAC audio files, Apple recommends the following specifications:
• Audio Format: Baseline Low-Complexity Profile with AAC-LC (Music)
• Data Rate: Up to 160 Kbps
• Channels: Stereo in .m4v, .mp4, and .mov formats
• Output Sample Rate: 48 kHz
• Encoding Quality: Better

I had the exact same obsession, and ended up creating a FLAC-to-iTunes importer that decodes FLAC files to WAV and imports them into iTunes using iTunes' own encoder: https://github.com/cbguder/FLAC2iTunes

It should be easy enough to modify FLAC2iTunes to support direct WAV input.

As for the soundcheck values, I compared iTunes, XLD and afconvert by encoding WAV files to AAC and decoding them back to WAV and comparing the decoded audio data. I also compared afinfo outputs for the encoded files. While the souncheck values are different for each file, the decoded WAVs are exactly the same, so even if you use XLD or afconvert, the chances are the resulting files will sound exactly the same.

For afconvert, I used the parameters suggested by Apple in the "Mastered for iTunes" guide, with an intermediate CAF file:

afconvert source.wav intermediate.caf -d 0 -f caff --soundcheck-generate
afconvert intermediate.caf -d aac -f m4af -u pgcm 2 --soundcheck-read -b 256000 -q 127 -s 2 final.m4a

For XLD, I used these settings:

Format: MPEG-4 AAC
Mode: VBR (Constrained)
Encoder Quality: Max
Sample Rate: Auto
Target bitrate: 256 kbps
Add gapless information for iTunes: checked
Write accurate bitrate information: checked