Rob,
Charging lead acid batteries in series is always superior to trying to keep them balanced/properly charged in parallel, so in that regard the 6 volt golf cart style deep cycle units are a good choice. I always used two of the 6 volt batteries in my camping trailer which got lots of cold weather use out during deer and elk seasons...and the battery performance was much better than using 12 volt batteries of similar total amp hours. The 6 volt cart batteries in the highest amp hour ratings are a bit taller than similar 12 volt units, so check your battery bay for enough clearance.
Since the total system voltage of the two cart batteries in series is the same as the two 12 volt automotive units in parallel, the performance of your RV systems (including starting the generator, if that bank is its source of cranking...) will be the same.
My Gulfstream diesel pusher had a third bank of batteries, independent of both the house battery bank and the chassis bank, just for the generator an inverter, and that third bank was comprised of golf cart style units...
Chuck
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2007 Tour Master T40C
Acura MDX toad
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