My gut instinct is that micromanaging the order in which people in each group get on will only add time and confuse people. If you assume that maintaining the recognition aspect of the boarding order is the most important part to DL, then it's a tough nut to crack. I would recommend two small changes:
1. Let PMs board with C+, since in theory they should get C+ at booking if available anyway. At stations like ATL, this will lead to some folks in the C+ boarding group going further back.
2. Let folks with the Reserve card board with SKY (realistically they probably aren't in Main 1 anyway, but there may be a decent number of FOs with Reserves).
Past that... I don't know what can be changed and still make people feel good about what they paid for or how far they flew. Maybe on some of the flights from ATL that are known to be bad (e.g. 757s), start boarding through the rear door as well?
Theoretically if they did ComfortPlus1 and ComfortPlus2, Delta would offer the same “recognition incentive”, with it being split into separate groups. How you differentiate on who gets in C+1 & C+2 is another discussion, but perhaps paid C+ in the first group and upgraded C+ in the other, to incentivize medallions to buy up?
As to your other suggestion, maybe they could create Sky1 and Sky2? With Sky1 being PM&GM, and Sky2 being FO and Amex reserve. In that case, effectively Sky2 is people currently boarding in Main1, but doing that would help split up the massive Main1 group. It also would incentivize infrequent flyers to get to FO or get the Reserve Amex, while still keeping the “early” boarding in Main1 for the other Amex Card holders.