Are bike shoes that much faster that it's worth changing shoes twice?

Changing shoes only adds 10 - 15 seconds to my transition time but I feel it saves me a lot more time then that over the entire bike course.

In terms of energy transfer, you will definitely benefit by riding in cycling shoes and clipless pedals. Toe clips will help and definitely go with them if they are your only option right now, but seriously consider moving into using a shoe/pedal system. Is it a pain to change shoes twice? A bit. However, with practice... you can eventually master the snazzy T1 mount with your shoes already clipped in. So basically you exit the swim, put on your helmet, and exit the transition area. Mount the bike, start pedaling and then get your fit situated into your shoes. You can do the same thing on the dismount OR you can dismount regularly and just change out of your shoes before you put your running shoes on. Lots of options! No matter, though, cycling shoes + pedals will only help... never hurt.