You may have gotten a good deal from your dealer but you are not getting good advice. Most importantly, if you really have two different size batteries (a 200 amp and a 100 amp as bank1) connected in parallel, you have a problem even before considering the charge rate.
Change this first so you have equivalent batteries. Should be easy enough to just switch out the 100 amp o be used as a start battery and connect both 200's in parallel.
Next, can we assume by "generator" you mean alternator?
If so, what is the regulator? Is it set too low? Need more info as the regulator determines the charge rate.
Next, what is your shore charger? Rating? Ability to control bulk charge rate?
Lastly, What meter are you referring to? Is it calibrated? when?
Also, understand that a good regulator or shore charge will sense existing battery state and adjust charge rate accordingly - that said, a fullly charged bank will not have a high rate of charge as you described.