Security: There can be a private company in the future that comes out, and offers to secure these Bitcoins in a undisclosed , safe, offsite location. They can also opt-in to secure these funds up to a certain amount, sorta like how FDIC insured banks are insured today.
Mitigation: It is not Bitcoins fault that people don't know what they're doing. Once again read my statement above to understand how issues of safety and mitigation can be handled.
Transparency:
IT IS NOT BITCOINS FAULT THAT MTGOX CHOOSES TO KEEP EVERYTHING BEHIND CLOSED DOORS. IT IS MTGOX'S FAULT. If you want transparency go
http://blockexplorer.com, if not send MTGOX's support an email with your complaints. Thanks.
I already acknowledged these things are mostly not Bitcoin's fault. In order to be successful, the infrastructure built around Bitcoin on the whole has to be up to snuff. That is the point I'm making, they will hopefully be existentially pointless arguments in the future but they are valid right now.
Security: No such service exists, only time will tell which hypothetical ones are actually secure. Moreover this is not a catch all for end-user side security.
Mitigation: I don't think some of the people that have claimed to have had their wallets stolen would say they didn't know what they are doing. Risk mitigation is very hard to do in practice. On the other side people securing their wallets presumably inadvertently destroyed their wallets. True or not, these stories are warnings that we need many solutions for many needs.
Transparency: My point is transparency is not guaranteed because of defacto Bitcoin services that operate like mtgox. This is why I feel it is important to emphasize the voluntary nature of Bitcoin between users and services.