there are several camps on this topic
there is dc and then there is dc , same as for ac
there are pro's and con's with any type of voltage
high voltage dc buss systems have lower losses but generally speaking have very large strings of batteries which require more careful maintenance and looking for a weak cell. also there are issues with serious injury with high voltage whether or not it is ac or dc
high voltage dc can have serious consequence if you develop a bad cell, think big explosion!
personally i think that 48 vdc is the max i would look into, it is a good comprimise between safety, maintenance and wire sizing,,, and there are quality inverters already available
lower voltage systems such as 12vdc have gone out of favor for most folks, but there is a place for them.
12vdc systems are far easier to maintain and in many ways safer, not much shock potential here.
depending on the system and its purpose, the ability to split off circuits and run smaller and cheaper inverters works well for some installation, redundancy is the key word here, and having cheaper modified square wave inverters one can have a few spares to swap out very inexpensively.
in a 12vdc system the bus wiring has to be quite large, but with carreful design wire runs can be made short enough to make this not as big an issue as some would make you believe.
then there is the issue of charging and how you are going to go about it, whether grid, wind , hydro, genset or dilithium crystals
to answer part of your question re generator or alternator as it relates to automotive components
forget the generators of old, they are robust enough but of poor efficiency, and also forget the average car alternators, they too are not very efficient and most have internal regulators which are not optimal in any application for flooded lead acid batteries.
if you want to use automotive alternators, think about hd truck units of the large frame families such as prestolite loadhandlers or the large leece nevilles or if you got the bucks go with an electodyne alternator. with these you still scrap the regulator and go with an external controller such as the balmar, xantrex or amplepower units. these units take control of the alternator and have temp sensors for not only the alterntor but the batteries to provide protection and temp compensation. they provide true three stage charging with equalization and are programable for all parameters from soft start to precise bulk, absorption , float voltages and /or time based. personally this is the option i like the most for various reasons mentioned among others.
some of these hd alternators can provide very decent efficiency, relatively low speed charging and have very hd bgs along with being relatively user friendly for repairs. also i should note that ebay usually has many to choose from well worth the money.
another thing to keep in mind is total system efficiency, don't get hung up on on part of the system because of a reported efficiency rating of a single component. what you want to be after is overall efficiency of the complete system and there are many factors to consider.
for instance, one inverter/charger might advertise their inverter as being 95% efficient, but at what load? and then again how efficient is the charger section? if the charger is only 75% efficient then you certainly have to factor that part into the overall system performance efficiency.
another example, is how the batteries will be charged, flooded cells can take a large amount of current from about 50% to 80% depth of charge, but from 80% to full charge they cannot take but a small fraction of the amperage and must be tapered back as they top off. in other words the last 20% may take 10 times longer to charge than the first 30 percent. this last 20% will take a very long time and if you don't have good efficiency from the charging system it only compounds the efficiency problem.
another concern is conversion, you want to limit the amount of conversion you go thru, it makes little sense to generate, run thru and inverter charger then to a battery to charge when you can go from a dedicated alternator direct to the battery in many cases, most especially if you are using an inverter/charger of unadvertised or relatively low efficiency on the charger half of the inverter charger.
the answer to your question is there is NO right answer that fits all installations, each installation has peculiarities of its own that require different approaches. folks will argue this till the cows come home.
the one thing that everyone will agree on though is, conservation first.
every watt you don't burn is one you do not have to generate, convert, store, reconvert and transport
plain as mud huh?
bob g