ICE - C/A-A-A Dirt cheap, able to be built on most worlds, and widely available. As noted in the TechManual, they use many of the same parts as industrial ICE systems, so successfully sourcing spare parts from local industry is likely very effective. Also, given how ubiquitous ICE is, finding fuels should not be much of an issue. I would imagine that modern ICE systems would be extremely flexible with the types of fuels used. Improvements in material sciences should also yield lower maintenance needs when compared to real world combustion engines. Final verdict: they make complete sense for militia, budget forces, and tech-strapped SW-era armies.
FCE - D/C-D-D Twice as expensive in raw C-Bills when compared to ICE, but half as much as a fusion engine. Now, there are some real advantages, but there are logistical considerations that make ICE more attractive. First, FCEs are more complicated and MUCH less common that ICEs. Good luck foraging for parts. Second, 'exotic' fuel usage. Yes, hydrogen is "free" if you have a fusion engine and water. However, we have no idea how fast a fusion plant can make hydrogen. We do know that the existing logistics for ICE is better and that water is not necessarily abundant.
There are other issues with trying to keep a primarily FCE force topped off with fusion units. For one, losing your fusion engines becomes much worse, as their loss can strand many more units. Second, at the very least the fusion units will have to stop to make fuel. They don't have large storage tanks for water and hydrogen, right? Therefore, you lose your operational tempo when compared to pure fusion forces. FCEs might even lose out to ICEs if there is enough local fuel (i.e. gas stations & truck depots)
Final verdict: FCEs are great when you can support them, but that means new infrastructure. Post-Jihad, it seems that most factions are operating defensively and cottage military industry has sprung up all over the place, so FCEs work. I wouldn't want to try to run a 4thSW-style blitz using FCEs though.