I'm still waiting to get my road bike, but I upgraded the rear wheel and cassette on my mtb about 6 mos after getting it and it made a huge difference. Ride the shifters until they break or you get tired of maintaining them. Change the wheels first if you do anything. Synapse is a nice bike. I rode one several times trying to decide what to get.

I too started wirh an entry level bike, Felt F90, and yes its ok to upgrade if you like the bike, I started with brakes, first Koolstop salmon pads, later Cane Creek SCR5s, used off ebay, big improvement.
Next was wheelset, Neuvation M28 AERO3s with kevlar bead tires, this made a huge difference, $250.00 plus tires, then after checking around local bike shops I came across a lightly used Tiagra 9 speed groupset including crank, got it plus installation for $215.00, this included a new Ultegra bottom bracket.
I now have an entirely different better functioning bike that I will ride and enjoy for a long time, it is unlike any other because I choose the component mix and that makes it mine.

It's been known that if you change out the Sora STI caps for some Ultegra ones you increase you wattage by another 100W! :)

engine
saddle
engine
wheels
engine
shifters
engine
r. derailleur
engine
etc. etc. etc.