Hello,
here are some answers to your questions:
#1 What is ganed by migrating over from PPPoA to PPPoE and advantages if any?
PPPoE induces slightly less overhead than PPPoA (except if you are running PPPoEoA) and does not require any ATM connections. It is thus easier to deploy.
#2 Can you run both in Parrallel? Can PPPoA and PPPoE even exist on the same router?
Yes, you can have both running at the same time. The only thing to be careful with is if you are running PPPoA and PPPoEoA (PPPoE over ATM) towards a specific customer, those would require 2 separate PVCs I believe.
#4 IPv6 advantages? Our company although small is taking IPv6 very seriously.
At the moment, using IPv6 only prepares your router for "the future". There are no yet any specific bonus to implement it apart being ready.
#5 Caveats or Problems?
Anything is possible ;-)