I had upgraded my Onkyo HT-S3400 few years back.
- Fronts moved to surround
- Added Onkyo SKF-4800 towers as L+R
- Replaced Center with a new center Onkyo 309C(got from Japan through a friend).
Obviously sound quality improved by many notches.
After few yrs of upgrade, the AVR(HT-R390) went bad(no sound issue). With no repair possible, due to non-availability of the parts, I had to upgrade to Yamaha AVR(RX-V585) with it the sub woofer to Bic F12 as the new AVR doesn't support passive sub.
You may upgrade your Fronts & Center to Pioneer(SP-FS52 towers + SP-C22 center). I read somewhere that few of the FMs have upgraded Onkyo HT-S3400 to Pioneers.
However, availability of pioneers is an issue these days. So, keep your options open and explore other speakers.