The thing I like about the FS is that adds a unique dimension to naval defence. As it stands right now, naval operations are pretty plain compared to land attacks, where you have to consider attack and armour types.
As far as specific units go:
A popular recommendation is to replace the FS with a fast/cheap/light-LS version. With the rebalanced trireme it acts as a fast attack ship (albeit not the cheapest). To me this feels like just another attack ship and it's gonna get lost between the LS and Trims. So I wouldn't want to see that.
Another one was a slow heavy dreadnaught type, lumbering naval behemoth. I could see the viability of this one as you're sacrificing speed for firepower (these would make great CS escorts in revolt worlds). This one I like a bit more, but I'm not overly keen on just another attack ship with a different attack-cost-speed balance point.
I definitely don't like the heavy-floating-defensive-fortress option. As it is people turtle up pretty good with biremes, do they really need something that makes those turtles bigger?
I think my favourite idea is the Catapult Ship (Essentially a naval equivalent of the catapult .. can attack ships as well as walls/buildings. Maybe even strike land units inside the city). However having an alternative defence ship would be nice.
What I would really like to see is to have the some kind of attacks diversification in the sea, similar to the land, i.e. ships with ram attack and ships with range attack. Some ships would be better against ram attacks, some would defend better against range. Range attacks could hit the city/walls/land units. In return catapults could play a defensive role against incoming naval attacks, by having not just land range, but also naval range attack. .. but I suppose that's beyond the scope of this RFP