The issue with scaling up fuel cells is that they require even more rarified metals, as I understand it, the amount of platinum (and other metals) you need doesn't scale up in a linear fashion. Once you get to heavy machinery, from large trucks to super-panamax ships, you're talking about a significant expense on precious metals alone, not to mention the extra engineering that goes in to storing a useful amount of hydrogen.

Combustion, especially in a medium that allows you to control the burn rate, is a much better option. It gives you more power at higher density without the downsides of hydrogen storage. Mixing hydrogen with diesel is one option, but there are some cool things being done with Ammonia (NH3), including mixing it with diesel, or cracking off some of those Hs in liquid ammonia solution and using that as fuel. The great thing about these fuels is that, much like biodiesel, existing diesel/bunker engines can be adapted to burn these fuels.