There are tradeoffs (strengths and weaknesses) with any AIP system including fuel cell. It is significant that Japan and India's DRDO appear to be interested in developing their own fuel cell AIPs. Australia relies on lead acid batteries (LABs) with no AIP for the Collins and with improved Li-ion batteries (LIBs) Australia may not choose any AIP for the future submarine.
Geoff Slocombe writing for ASPI's The Strategist on June 18, 2015 has authored a thought provoking article on many aspects of submarine function, particularly AIP systems and LIBs. Geoff Slocombe's article was first published at http://www.aspistrategist.org.au/air-independent-propulsion-is-a-must-for-australias-next-submarines/ :
"Air Independent Propulsion is a must for Australia’s next submarines