I think BTC-e is legit. They're just swamped with recent deposits so it will take time to catch up with the paperwork and regulatory compliance.
I spent my funds on btc-e while waiting for my funds to clear at Bitstamp, which just cleared yesterday. It's about 10% cheaper to buy coins at
btc-e, so I immediately asked Bitstamp to return my deposit. I'll wire the funds to btc-e where I can buy cheaper bitcoins or ltc and other cryptos.
Don't be scared to use btc-e! A $80-150 discount per coin is worth the risk IMO.