Hi Ryan,
One thing to note here in relation to Cork routes, the interlining agreement is already up and running on the Dublin / Cork route and it is not part of the Aer Lingus Regional agreement. While the connectivity isn't ideal, Aer Arann also have commercial issues to consider when scheduling the flights (i.e. Ryanair).
I think a note on the presentation is key....if you look under the route map it says "Phase 1". We may see the connectivity in general across the network improve as both EI and RE progress along the scheduling learning curve.
All the best,
P2C