I think sine waves make a lot of sense in additive synthesizes, but in a subtractive synthesizer like the SID, good waveforms span a range of frequencies, so composers can target the filters at them to produce all kind of custom waveforms. The sine has only 1 fixed frequence, so there is nothing to subtract from it. Therefore, it doesn't make that much sense in an subtractive synthesizes.
Super saw sounds good! But what do you think of a resettable sawtooth, like in this picture, the bottom most one:
I think this one could be very usefull waveform addition: You could reuse the pulse-width register to specify the moment of restart inside the waveform, and that would also automatically allow people to change it while the note plays, just people do now with changing the pulse width during a note to create all kind of sounds. It will also have lot of interresting frequency properties, which you can target filters at, to get exactly those you need. And it would also be reasonly simply to implement.
A second form of noise sounds good too: It would both help in creating better sound effects and create more possibilities for percussion instruments.
I think if the SID would be enhanced, and I think the Mega65 is in an excellent position to do so, some brainstorming would be usefull to see what features are most usefull to add. You could do it brute force, just add more voices (like the 1541U2 does), and while it absolutely makes sense to address the SID's worst limitation, just adding more voices alone is not probably not the best way to enhance its music capabilities.
I think just a few additional voices, 2 or 3, would fix the worst limitation due to the amount of voices. The difference between 3 and 5 is a lot bigger than going from 5 to 8, like 1541U2 has. So 5 or 6 voices make sense. The register space (and FPGA space) saved could be used for additional waveforms, and I think a second filter would also make a lot of sense, so you can have full waveform freedom on a second voice.