My own experience is that full remastering is so quick and simple for me, that I rather do that than creating incremental modificatons. As for persistent store backup, I would guess that rsync -axu to another loop-mounted image should work just fine. In case a full file copy is deemed to take to long. If day-to-day modifications are not too extensive, using a subversion (or git) repository is also something to think about - then you will also be able to go back in time to any specific time you have checked in.

As Werner noted, use/not use of persistent store does not seem to affect boot-up times very much (DVD version). So in my use case, time would not be an important factor for choice of method.