Cannondale Synapse Hi-Mod (2016) - What to upgrade?

The frame...

Buy a shimano tl-cn42 chain wear checker

and probably shortly after a new chain! I like Kmc ones, your mileage may vary! (Quick link open and close pliars are good and a chain holder or use a metal coat hanger)

buy some vittoria latex tubes and conti 5000 (or 5000 tubeless and don't buy the latex tubes if your wheels are tubeless, I think they are but check) 

buy a power meter if you're in to that sort of thing, don't if you aren't.

buy some rock and roll gold chain lube

....curious as to why you guys haven't taken a hacksaw to those forks protruding through the headtube? That'd be my first upgrade.

Hi. I have a 2014 Synapse hi mod and its a really fun bike and I really enjoy riding it. I run Enve AR 4.5 wheels but they are a pretty expensive upgrade and they run tubeless. The wheels that came with your bike are pretty high quality. Yours was a pretty hi spec model when you brought it, so it shouldn't need much upgrading. Good quality tubeless tyres might be one way to go but even good quality clinchers. I would repair brakes and any other issues and ensure its serviced.
Hope thats been helpful.

As above, decent tyres first and replacement chainring (like for like, no real benefits from anything else). The bike needs little besides so don't waste your money. If you have a desperate need/desire to burn money then spend a grand on a gravel bike that doubles up as a winter trainer, complete with decent mudguards and approp tyres fitted.
Ref the top stack slicing...have another look at the setup before you do. It looks to me like the classic mistake of trying to go low but finding it uncomfortable. The bars have been rotated up to compensate for an over dropped stack. Try moving one of the 10 mm spacers from above the stem to below it, and rotate the bars so that the shifters are flat. This will also help your reach to the drops.

Do the brakes squeal or pulse?  Are the pads badly worn? Do you find yourself wanting more stopping power? Is it still leaking fluid? Do the brakes.

Does the bottom bracket creak?  If yes, I would replace it after determining the root cause of the creaking.

Are the wheels true?  Are the wheel bearings smooth?  Are the derailleur pulleys worn?  All those nasty little maintenance items we all like to forget about...

Otherwise, as has been said, nice bike: ride, enjoy, repeat.

Ditching the Marathons for something like GP5000's would make it feel like a new, exciting bike. 

Also replace the outer chainring and slice that steerer, everything else is fine. 

If it was my money I wouldn't bother with the calipers personally.

Personal preference obviously but I'd go for Di2 or better wheels but TBH it's a nice bike so I'd be quite happy as it is.