Having recently tried to make a couple dragonmarked characters to keep boredom at bay, i found myself wondering why dragon shards, particularly siberys dragonshards aren't used as they are in PnP for dragonmarked characters.
In PnP a siberys shard can be used to focus or enhance dragonmarked abilities. It is even possible to have a dragonshard implanted (for a hefty price) to augment your character's abilities with the mark. I think this would be a fun option for making dragonmarked characters a viable alternative.
Perhaps change that initial blue haired girl quest in the harbor, from one who gives you a free feat respec, to one who gives you some sort of socketed item which you can wear (maybe a different item slot for each house's mark to make it interesting, like a socketed shield for house deneith, or a socketed tiara for house jorasco) that can hold siberys shards. More shards equal more abilities or more potent versions of the item in that slot. Obviously this would have to change per mark, a lesser marked character shouldn't benefit so much as a greater marked one does from the item. Another idea might be a new enhancement that becomes available to any character with a greater mark, at say level 14, that costs 6 AP or so and allows for the implantation of a perfect shard.
I think this would be a fun new addition to game play and would give players a chance to use all those flawed and imperfect shards they've collected over the months not to mention adding some extra eberron flavor. Just throwing it out there, feel free to agree or flame me.