Installing a condensing water heater can be a bit more complicated, especially since extra parts need installing (such as the drain). If you are renovating your heating system from one traditionally configured, condensing water heaters are not a straightforward solution.
You are going to need to install brand new gas lines as well as venting systems. Taking into account the hourly wages of plumbers and electricians brings the potential cost of this new configuration up to the hundreds of dollars range.