A lot of the Skyhold/keep stuff was either definitely cut or feels as if it had been planned to be bigger, then shrunk down on the final pass.
Skhold has a lot of interesting rooms with no apparent purpose (a sort of barracks-type keep about equidistant between the Inquisitor's tower and Cullen's room, an underground dining room/hall with zero furniture, a subterranean library with more bookshelves than the actual library).
Skyhold improvements are lackluster, especially compared to how richly decorated and improved upon the liberated keeps become compared to their appearance when first encountered.
Keeps don't really evolve or play any role in future missions, which is a huge waste and one of my major disappointments, as I loved the Keep concept. The feeling when Griffon Wing Keep is first captured and filled with merchants, soldiers and decorations everywhere was just magical.
There seem to be several places in the world that were intended to be keeps at one point in development, but then were scrapped when the Keep mechanic was pared back. Hargrave Keep flies Inquisition banners and is a great counterweight in the southern, most difficult to access part of an already forbidding map with only two Inquisition outposts. There are also bits of lore that imply its former prosperity, and you can dispatch and ally with the Avvar who would have claim to its vicinity. A similar situation obtains with Grand Forest Villa, which is a golden opportunity for a Keep conversion in a remote part of the Hinterlands, basically the Inquisition's backyard. And post-civil war, why not have the reigning Orlesian monarch grant the Inquisition Citadelle du Corbeau or Fort Revesan? In all of these cases, I honestly thought I was about to capture my first keep of the game, only to be disappointed.
All of the above are areas that I hope BioWare will implement in added content/paid DLC. Skyhold/Keep stuff is priority number one for me personally, as I love the "bringing order" and "helping the population" parts of Inquisition. To me, this is what gives the Inquisition and the Inquisitor legitimacy and a true legacy, not the Mark, which could have happened to any oaf.