I'm also an owner of a Fuji Gran Fondo 3.0 and all bias aside it's a great bike. I too replaced the saddle to a FIZIK Aliante and replaced the tape after the original was worn down. I got a lizard skin and love it. I replaced the Tiagra 10 speed cassette with a 105 12-27 (love the 16 cog in the middle) after about 5k miles.

I would not change anything else other than wheels and tires. Mine came with Horrible Hutchinson Nitro and I've replaced with Michelin Pro 4 Endurance and now Conti GP4000SII. Both are much better than the Nitros.
I also replaced the Oval wheels with cheap-but-oh-so-good Vuelta wheels. The combination of better tires and lighter wheels made a world of difference. I've tried for a while a friend's set of Shimano C-24 wheels and I liked it quit a bit.

The Gran Fondo isn't the lightest bike around but it's not the heaviest. With all the upgrades I have it now at 19lbs with pedals, bottle holders, cell phone holder, computer with cadence. Not bad at all.
A friend who has a 6.2 domane 5 times the price rode my bike and said he was impressed.

Seriously tho, don't wast too much money other than a wheel upgrade and this bike will keep you happy for a long time.