At the moment we are using just the core rules. We've done Revelations from Heaven using pre-generated characters to test the system prior to generating our own characters. Thoroughly enjoyable.
When we generate characters my intention is:
Allow everything from the Compendium/Armoury with the exception of the fighting styles. These are predominantly for fighters and, in my opinion, don't really add to the game that much. The other focus rules apply to hunting, foraging, social contests etc and affect all characters equally.
The rest of the Compendium is mainly extra skill info, general special abilities and crafting. Useful stuff for any character/group.
Combat special abilities aren't just the realm of the fighter. Even a mage can benefit from Improved Dodge, Stunning Blow etc. Whilst you can go mad with combat special abilities the limitation of only using a single basic and single advanced ability means you can't just take them all and stack them. Fighters can't be built like in Pathfinder/D&D with the intention of using all the feats every round.
Mages don't seem particularly underpowered to me, you just need to be careful with the AE. My player who wants to play a Guild Mage has already planned to max out alchemy and keep a sideline in magic potions. And improved regeneration III!
I have made one houserule: We play with low LP regeneration, d3 instead of d6. My ruling is that at any time you receive LP, KP or AE you can roll 2d6 (2d3!) and take the best one. It takes the edge off of the low speed of regeneration and somewhat mitigates bad luck.
I've learnt my lesson from the past and now only buy a system when it is complete, and playable. My bookshelves are weighed down with half-baked games from companies promising great things! I'm also careful with my expansions. Can anyone else remember the Unbalanced Unearthed Arcana from AD&D first edition
Without the Compendium the game is, in my opinion, completely balanced. As long as I'm careful with what I take from the Compendium that should continue.