For my games, I've found it useful to use the 3.5 versions of the gods, with slightly modified versions of outsiders, elementals, dragons and monsters.
I've done it this way due to the ease of just using stock 3.5 (and to a lesser extent PF) creations straight out of the book. The more I have to modify to snap into an alternate definition the more difficult it is for my players to follow.
--Multiply this by the fact that I often run a game for a group who play in several games at once. Being the sole game that has a wacky list of gods, domains and outsiders can really throw them.
ALL THAT being said, I do tweak things as much as possible after that. While my players can probably expect red dragons to spit fire and white ones ice, they have no way of knowing what alignment that dragon may be. They won't know what powers, personalities or tactics to expect when dealing with these creatures either. It adds a little spontaneity and creativity to adventures when they still have to learn something beyond a simple knowledge (arcana) roll.
I spent a bit of a detour getting here... But as far as the cosmology, I use a modified version of the great wheel. Again, I use the wheel because my players would get messed learning something new just for my game, and because I use the default gods too.
However, I do the same thing for the planes I do for dragons. While you may expect Elysium to be good and Hell to be evil, I use all the tricks I've learned to make the planes as dynamic, mysterious and interesting as possible after those well known bits.
For example, mixing up the demonic power structure has been wonderful for RP options and campaign twists. The lords of hell have changed a half dozen times in a half dozen games, just because I want a different list.
The few things I have done which are completely new or unique to my games include; making archons LN by default, as opposed to Good. I have also added another plane (well a few but..) on the "material" axis, naming it the "battleground" and using it as such for when creatures of all alignments need to spar.
Oh, I've also slightly jogged how the planes connect to one another. For example, when one climbs Mount Celestia and reaches the top, they enter Elysium instead of just the last mount. Also, I've squished the good planes together and evil planes closer together, treating them more or less as two "infinite worlds". This has helped travel between them. It still isn't easy, but plane-hoping spells aren't necessarily required.
Kind of a half baked response, I apologize. I am very sleepy and operating off 6.5 hours of sleep over 2 nights. I should go crash now
