We played a 2 player game and it plays well. But I can see trying variations like keeping both god cards, or playing a 4player-like game where you play 2 hands and whoever has the highest combined score wins. Anyone else try 2 player variations? The game components are very nice but you need to bag the discs in separate bags or else you will have to sort a ton of discs before playing. Then you have to jam them into the compartments. I'm tempted to invert the insert for easier storage or get rid of it completely.
I have played four two-player games and they seem to work just fine without any modification. I am baffled why they chose to add a warning in the rules that two player games might not work so well.
We bag all of the size 4 races together, size 3 races together, etc. and put the leftover counters in one bag together. That way, they are easy to separate before a game but you don't have to fiddle with too many bags.
We keep the cards, dice and grey cubes in the insert. We keep the bags of tokens underneath the insert.