To get deep cycle, marine quality AGM's in a large bank, I think that 4D's are cost effective if you have the room. We have 4 Lifeline 4D's in two banks which are constantly linked (except if one battery should go bad) as our main house bank. Then we have two dedicated Optima spiral AGM's as dedicated engine and generator starting batteries. The Engine starting battery circuit can be linked to the House Bank (with a special switch).
For shorepowe charging: The Generator start battery is on a controlled trickle charger from the Mastervolt inverter/smart charger; and Engine start battery is connected with a reliable and inexpensive Yandina combiner. The generator battery gets generator driven charging from it's own generator alternator; and the engine has a 50 Amp Delco with its own smart regulator in addition to a 250 Amp Balmar with a smart regulator to charge the house bank.
The Mastervolt (unlike others) is rated at 100 Amps of smart charger capacity and actually puts-out a reliable 100 Amps.
Our boat was set-up when we bought it from J/Boats for the House and Engine Start Batteries; and the alternators. We added the seperate generator battery and Yandina combiner. The only other change was to upgrade from the Heart 2500 Watt inverter/130 Amp (really 60 Amp) charger to a MasterVolf 2500 Watt/100 Amp inverter/charger.
Yes, we use a lot of juice when we're in offshore mode with gps/radar/computer/chart plotter/instruments/refrigeration/lights,cameras, action mode. ;^). But then the 7 KW Westerbeake generator uses about a 1/2 a gallon and hour or less -- it's all irrelevant when we motor, because the Ballmar really charges the batteries pretty quickly.
If you drain down the almost 800 Amp Hour main bank, it does take a while to "fill it back up" (as you note, RoverHI). There's not free ride for such consumption.