Which offers the best/most protection for a boat that will live in freshwater? Assuming that the anodes are changed every yr.

I utilize my factory Mercathode along with a set of Magnesium anodes on the drive with great success in fresh water. The Mag anodes eat away very fast and the galvanic corrosion does not even touch the drive in most cases. The Mercathode helps also. The more stainless on the drive the harder it is to keep it from corroding. A drive shower, 4 blade prop and remote resevoir line all put more stainless near the drive.

I went the cheap route last year and used aluminum anodes and had some minor surface corrosion on the drive vs using the Mag anodes where there was none. The Mag's are worth the extra money.

If the boat is going to stay in the water, then use both anodes and the mercathode.

Guess I'm not very clear.

I'm only talking about the lower anode that is mounted to the gimble assembly where the hyd hoses are connected. My new Alpha transom units have the anode. I'm considering swapping that one out for the Mercathode system and still using all the other anodes too, if the Merc unit is better.
The replacement of worn anodes or the drain on the battery is not a factor here.

Currently has SS props, but changing them to Al props do to the higher corrosion from them.
Thanks

If the boat stays in the water and is hooked up to shore power a galvanic isolator is a good idea too.

Yes and yes.
It does have the isolator too.