Most new WH's are taller than those of old because of the burner designs (at least on gas appliances). It is somewhat rare when a new WH can go into exactly the same place as an older one, those in electric have the highest possibility, but even then, not always possible - the wiring may reach, but you may need to move the supply lines. Where allowed, flexible water lines can make that easier.
A condensing unit will use a two pipe system that can either be two actual separate pipes (and often starts out that way, regardless), that may terminate in a concentric design. The distances and pitch of the lines becomes much more important, since the condensate must be able to flow back towards the unit, where there's an outlet to collect it. THen, since the inlets are often lower, you have to be careful about where they are located, and what else is around (for example, the inlet shouldn't be near a dryer outlet and the exhaust has some specific offset distances from operable windows and doors). Those lines can't be too long, either.
The good thing, is that most installation instructions actually are pretty good. The bad thing is most don't read them and, they are different. Not that people don't install the existing ones properly all of the time.
