Posting again to say that I now have a new idea as to how Social Links should be done, or more correctly what they should accomplish, since I've decided this game will be going with only-one-Persona-per-character-except-for-evolutions.
The basic idea would be that each 'rank up' you get in a Social Link gives you one point, and with ten ranks per S-Link this would amount to a total of 200 points (obviously not including the World Arcana and your own Arcana, the latter of which determines Persona evolution). Once you'd have enough points, you'd then be able to exchange them for Persona abilities, elemental upgrades or special items. I was thinking at first that this could be done in the Velvet Room, but then I thought that this sort of thing would be a lot more in line with the Time Count's services present in Persona 2, though I'm still leaning towards the Velvet Room as Igor would probably be more familiar and bearable.
Obviously though you couldn't just buy any skill even if you did have enough points, certain elemental affinities wouldn't allow it. This point system also wouldn't make any distinctions between what Arcana Link you got the points from (except in the case of S-Link completion) as that would be too much work, especially for a freeform game, though this all would be easier than just coming up with all the different personae for each Arcana.
What do you think?