The comparisons being made in this thread aren't apples and oranges, they are more like apples and Toyotas.
1. Poloniex uses Cloudflare for DDOS protection. You would not see the site using the same IP address over time.
2. The Mtgox problem has/had nothing to do with end user authentication. You definitely SHOULD set up 2FA anywhere and everywhere that is important to you. However, that will not prevent an attack against any exchange's back-end systems.
For whatever blockchain-based currency you are holding, if the keys reside anywhere other than offline storage, then there is a vulnerability. The severity depends on where those keys sit. If your currency is sitting in a virtual wallet on an exchange, then you either trust that exchange has a security posture that is worthy of a financial institution, or you don't. From a risk perspective, a virtual currency (VC) exchange should have higher security and more due diligence than a bank. With a bank, there is the possibility to roll back fraudulent transactions, and some amount of government protection (in the US). With VC, done is done.
Would I trust a few hundred dollars in an exchange such as Bittrex or Poloniex? Sure. A few thousand? Probably. Tens of thousands? No way. That is not an indictment of any particular exchange; it's just that there are risks that cannot be mitigated if someone else is holding the wallet keys.