I've never seen an upgraded mark in play, but I've heard that they don't stack with your base mark, even if they are the same element. I think a reasonable change would be to make it so that upgraded and unupgraded marks stack with your base mark. That way, upgrading a mark would be more useful than it is now; nobody seems to want to upgrade a mark because of this, and I wouldn't upgrade one right now, unless I had 7 of it.
Not that very many people will have more than 12 of a mark anyway, but keeping them limited to 6 per deck seems fine to me. They do provide that small advantage against earthquake/trident, even when they aren't completely indestructible by stacking with your base mark.