Maine Sail - the queen could have her dinner served in that battery compartment it is so clean. I am envious.
Seanymph - I have a 2001 Hunter 320 with a Protech-4 model 1230 charge that I believe was factory installed. It is not the best charger, but it is a mutli-stage charger. It would be interesting if this charger is overcharging your batteries, meaning a major product malfunction. Now, I rarely use the Protech charger. I charge with a solar panel with a very good solar charge controller, because there is no power in our marina (long New Orleans story).
As the others said, if I had money only for either top of the line charging equipment or great batteries, go with the charging equipment. Good batteries will be gone soon without good charging. I have a Balmar 70 ALT w/ ARS 5 regulator with temp sensors on Batt and Alt. A Balmar Digital Duo for dedicated starting battery. Last, a very good, temp comp solar controller. My weakest link is the ProTech 4 charger, which I only use cruising during short stays in other harbors.
As for batteries, I went with 4 Trojan AGM Group 27 (3 house, 1 start) in the port settee (after being a GEL battery man). Basically, the best price per amps on low maintenance batteries from a well respected manufacturer made me go with Trojan AGMs. AGMs have some good points, their low maintenance, can tolerate the charging voltages of the stock Yanmar alternator (Hitachi model LR155-20, 55amp), and low self-discharge rate. Now, the stock alternator is not a great charger with its internal regulation, but can be used to put something in the batteries. Do not go Gels unless you do some changes to the stock alternator to control the charging voltage. Gel batteries require unique charging voltages from Flooded or AGM.
To prevent the cooked batteries smell, go get a good multi-stage charger like the Truecharge. This will protect any investment you make in your batteries. Go with AGM batteries, if you want low maintenance and do not want to put money into changes to the Yanmar stock alternator. Gels are great, but you have to have a charging system designed for them. Hope all comes out well.