This is a personal preference only. The PRS seems to be less affected by choppy conditions. The nose cuts through wind and waves much easier and without affecting the pitching (nose up and down) of the craft.
If you get a craft with the surf rudder, the control is much better as it is never lifted clear of the water. Most paddlers realise the nose coming out of the water as they can see it but often forget that the same is happening behind them. This is particularly noticable when catching waves as any ski with a trailing rudder will lose it's steering as the rudder is a foot clear of the water.
The preferred way to catch waves (but way less fun) with any of the moloki shaped skiis is to let the wave beat you in the break and you paddle hard on it's back rather than riding it, especially if it's getting over 4 foot high.
With the Endorfinn and Spirit racing ski a flared nose is incorporated in the mould which do a fantastic job of stopping the nose from slicing into the water. While this is slower and uses more energy when paddling into wind chop or out through a break, it is the only thing that is going to save you from nose diving into the sand and a HUGE stack if you manage to catch a sizeable wave.
When I had an Endorfinn I'd always go for a paddle when a huge NW was blowing as the waves would be over 2m+ high and it was awesome fun catching these monsters as the down wave speed on a ski was unbelievably quick. I didn't enjoy it as much on my spirit racing ski as the stability wasn't as good as the endorfinn.
On my PRS i've tried it a few times and have regretted it every time as the nose goes to the bottom of the wave, keeps going straight down and I end up doing an end over end somersault which tends to hurt. If the waves are breaking on to sand it's just a matter of time before you bend the nose!
I now have an old Spirit cross trainer that I use for having fun on the waves when the swell is up. For all other ocean paddling I use a PRS and this includes going out into some really crappy seas. The stability really is that good once you get used to it. Awesome fun going in and out river breaks (Capel and Augusta) when the swell and chop are a bit nasty.
As much as I'd love an Epic 10 or Fenn mako, I don't see too many out on the ocean once the chop starts to pick up. (will concede this might come down to paddlers rather than the skiis. It might also be the fear of breaking or losing a $6000 carbon ski)

Hope this helps and apologies for being long winded
Peter

P.S. The ability of the PRS to cut through the waves makes grade 2 and 3 rapids (majority of our rivers) unbelievably effortless. Awesome boat!!!

We have a photo somewhere (I must get the oracle to find it) of one of the Bunbury guys who carries a Mirage 580 on a motorbike side car....