I will do my best- take my thoughts with the following disclaimers in mind:
I had been riding the 550 (before conversion to 701) for several summers before buying the FX1.
I have never ridden a stock FX1, RN superjet, SN Superjet (although have ridden a mod one), SXR, or 750sx/sxi.
AND These two skis are setup for different ideals-
The 550-701 conversion was setup to be my everything ski - long rides to beaches, carving local slalom ski buoys, hood tricks, subs, etc. Occasionally I would work on setup wakes and hit boat wakes, but I wanted a do everything at anytime ski. A Generalist Ski, for lack of a better word.
The FX1 has a high comp head, 144 pump and pump tunnel, shortened rideplate, mod b-pipe, SBN 46, wetjet Kraze intake, aftermarket pole/steering, footholds, MSD enhancer, other stuff. I bought the FX1 from a member on here (who bought the ski from the member who built it) because I wanted to get further into the flatwater realm (setup wakes, small nose stabs, etc) and work my way up to boat wake rolls (we have alot of wake surfing boats around here kicking large rollers). I have since toned back the idea of learning rolls due to a last summer (un-related ankle injury).
The 550 is jetted in a manner (correct or not) where the power is very stable over the whole throttle range, it will pull you our of a rear stand but is not really going to rip your arms off. Where as the FX1 is jetted for arm ripper. I wanted to have that "hit" of powerband.
The 550 is great - it is a bullet proof hull design that was around for many years. I believe that Yamaha's intention with the FX1 was to create a way to out 550 the 550 in the racing department. I believe I can actually carve (recreational-ly) better on the 550, than I can on the FX1. Probably has a lot to do with the extra weight of the waterbox/engine in the 550 now, then before when it had a stock 550 engine/waterbox as well as how each ski is setup.
I have the distinct feeling that I can ride the 550 for much longer periods, due to hull weight and standard ergos, compared to the FX1. The FX1 is constantly out of the water and skittish. However for just that reason, I want to "learn" how to tame it.
So in effect, I have the opposite feeling than you do regarding the FX1 "feeling" huge. But I mostly think that has to do with how each ski is setup.
Long Story-
When I first built the conversion ski - I only had experience on two other skis. One was a 650sx and one was a 550sx. I was enamored by the builds that people were preforming on the 550's (over at PWCToday, hadnt found X yet). People were putting the 650 and 750 Kawi engines in the 550 hulls. I loved the maneuverability of my 550, but I felt like I had to keep the revs high to enjoy it. While the 650 was the opposite, I felt like it had a solid bottom but the hull was heavy and felt like a boat compared to the 550.
I was out riding the 550 one day and was waved down by a guy on a SN superjet. We swapped rides for a few minutes but I could instantly tell that the SN engine was way better than the 650, but the SN felt lighter than my 650 hull (even though I don't think it is in reality). The guy could hardly ride the 550 and said he felt like he was trying to slalom ski. Come to find out, he had just refoamed the tray, put a rebuilt 61X, and added a coffmans, and redone the pump completely. I didn't know all this at the time and just thought the SN superjets were amazing stock.
Needless to say I wanted a superjet. The wife said 2 ski's max... and she loved the 650 for when she was putting around. I couldn't mess with the 650, and couldn't afford the prices for a superjet (also didn't want to give up the 550). About this time Rhaas came out with the 550 -701 conversion kit and I figured I needed a winter project - so here we are. Picked up the Rhaas conversion kit, 19pitch impeller, and a Wetjet Kraze from CList with a big hole in the hull for way less than a superjet! Then ended up getting the FX1 and sold the 650, bought a resto-mod 550sx, then sold it. Now with two kids, I am alot more limited on my time to tinker and despite how great both these skis are, the 550 doesn't get the attention it deserves.