Basic sound FX such as amplification/limiting, especially low pass/high pass filters, and (dream scenario) slightly more advanced FX like chorus, delay, and reverb could greatly improve sound/music quality and give us more freedom of choice in how we can use the channels. Since we only get one dedicated waveform per channel, this is even more important than if were able to use multiple of the same waveform in the compositions.
For example, currently the sine channel provides one of the better deep bass sounds, but to relegate the sine wave to that job and lose it as an instrument seems a shame when simply adding low pass to any of the other waveforms could create a similar or better sound.
Likewise, the same FX applied to the in-game sounds could also open up much more range.
Thanks for reading!