According to the IEEE transactions information (tar file here contains IEEEtran_HOWTO.pdf along with the class files)
Axel Sommerfeldt’s modern and actively maintained subcaption.sty package [23] can not be recommended at this time because it does not provide an option to prevent the underlying caption.sty from taking control of main caption formatting away from IEEEtran.
Instead they recommend using subfig invoked like this \usepackage[caption=false]{subfig}
Are there any plans to add a caption=false flag to subcaption? It seems that subfig has not been touched since 2005, so I would rather stick with subcaption if possible.
EDIT: There is a workaround posted here, but it involves re-defining how captions should be formatted, which seems to partially defeat the purpose of using a supplied style file.
subcaptiondepends heavily oncaption; there's no way to make it work without it. In my opinion IEEE should rewrite their styles withcaptionand not reinvent the wheel. – egreg Jan 16 '14 at 16:58