I would recommend leaving psykers until the wizards get put in vanilla. Then, you'll have something to work with.
I'd also recommend making Carnifexes and the like Semimegabeasts. Why? There are even bigger creatures about, in a whole different category:
http://warhammer40k.wikia.com/wiki/Titan.
I like the idea of adding in the daemons, but
how about replacing each HFS type with their respective Greater Daemon? The Frog Demon definitely fits Nurgle, vanilla Demon fits the Bloodthirster, Tentacle Demon has got to be the Keeper of Secrets, and the Spirit of Fire could be replaced with the Lord of Change (it's the closest fit).
As for civilizations, I'd suggest the following:
Imperial Guard (with both above-ground military base style constructions and below ground bunkers and bases)
Space Marines (similar to Imperial Guard, but with cathedral style structures as their above ground bases instead)
Sisters of Battle (same as Space Marines)
Chaos (generic, for wild forces and the like. Would live around warp portals, which would spawn them. The landscape would probably be quite Mordor-like as a result)
Khorne (Think Space Marines, but with a lot more blood)
Nurgle (Ditto, but also with filth)
Slaanesh (Ditto, but also with filth and "unknown substance")
Tzeentch (Similar to Space Marines, save maybe a bit weirder looking, the kind of structure that drives you mad if you stare at it too long)
Orks (with Grot slaves. Live in fortresses made of scrap with big garages for their vehicles as well as smaller desert-tribe style camps.)
Eldar (aboveground, pretty looking cities made of wraithbone)
Dark Eldar (think Eldar, but also has the look of a Chaos cathedral mixed in, and is all dark)
Tau (similar to Eldar, but not made of wraithbone, and more square/Japanese-esque)
Necrons (think a big crypt)
Tyranids (big hive)