Invest in a hardware wallet like Trezor and store most of your coins in there, until you are ready to trade. Do not send all your coins to any of the exchanges at once. Send some small amounts and trade them and rinse and repeat until you have accomplished your goals.
We first saw Mt Gox and now Cryptsy, so it seems these exchanges just cannot get their act together even though strict regulations are enforced since the Mt Gox situation.
There are no strict regulations enforced on these exchanges. That is the problem. If there were, they would've reported the thefts a long time ago before even trying to fix the situation. Several other exchanges did exactly that. Disclose that hey were hacked, and present a plan on how to recover the losses and reimburse everybody.
Biggest problem with the exchanges still seems to be social engineering and bugs in the engines. Even controlled banks lose millions each year due to human error, which shows that it is impossible to make a perfect system and stuff like this can always happen. The challenge for the exchanges is to minimize their losses in case this happens, e.g. by having low value hot wallets.
That said, try to store as little on exchanges as possible. Especially the smaller ones that have not been around very long. The bigger ones are now much more strictly regulated and have learned to take security more serious.
