There is a slider in the interface tab of the options screen that sets which zoom level the iconic interface kicks in. You should be able to adjust that and get back to the pretty 3D look.
I hauve noticed that if you spend the excess ability points for a standard race you lose some of the default abilities--they can't be generated by the custom race points system. It is unintuitive that your modified standard races becme the new default and frustrating that you can't revert them from within the game. It's livable for me now-I'm going to use the custom option from now on if I don't want a default.
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