There is NO loss of sound quality going through the Aux In connection David.
A better way to control the IPOD itself is through the RF wireless remotes available from I-jet.
They also have one with an LCD display which is easily adapted to 12V systems.
iJet Wireless Remote With Bottom Dock
The main thing you lose by going to an Aux Input is charging
capability for the IPOD which may or may not be of concern and can easily be dealt with separately.
Anyone interested in putting together a DECENT boat system without paying through the nose might be interested in reading my posts on this thread
before selecting anything. It might save you some money
and get you better sound.