Just a few things to consider to start...
A couple of key differences on these two is (1) how bad do you want a cockpit (3SR); and (2) how do you feel about the galley up model (4SR)?
Both of these boats make great liveaboards and have an abundance of storage. I’ve seen more than one take the 4SR, galley up model and turn the smallest stateroom into an office, and I’ve seen some take out the crew dinette and make a desk or large dresser there.
Others folks have a MUST HAVE attitude towards a cockpit. I wish I had one, but I’m not willing to give up my 4SR, galley up model in exchange for it. I’d like to just add a cockpit instead...have my cake and eat it too.
Neither of these boats, to the best of my knowledge, have walk-around decks which is something I’d really like to have. I’m talking about the Series I - I don’t think any of the Series II were made in the 4SR, galley up model.
Galley up means whomever is doing the cooking can still be a part of the crowd and enjoying the company rather than being stuck downstairs in the galley, away from everyone else. This also means that your galley and its occasional mess is right there on display in front of everyone, too. Everything is a compromise. You’ll enjoy replacing the galley appliances in a 4SR galley up model much more than you will in the 3SR galley down model.
You first need to determine whether a cockpit is important to you. For example, do you have dogs that are too big to carry who will need to get on and off the boat and into a dinghy from time to time? If so, then you need a cockpit.
My recollection is that the 3SR, cockpit motoryacht version has a smaller master SR due to the existence of the cockpit. They had to take that space from somewhere. Still, both boats have an abundance of storage. If you’re comparing strictly storage capacity, then the 4SR, galley up, probably has more. If the cubic feet of storage is driving your decision, then you have too much stuff!