Synapse - 2016 carbon ultegra or 2019 105 disc

Go for the 2019 model, the Synapses had a major revision meaning you have a much wider tyre clearance on the newer model so if you fancy doing some light gravel or tow paths you will be able to do this as well. As it's your first road bike you are better going for a slightly better frame and forks and a slightly cheaper groupset. 105 is excellent stuff and I honestly can barely tell the difference between my 105 set up and my Dura-Ace. 

Bear in mind synapses don't come with the full Shimano groupset*.  Does the ultegra version still have the OPI spider ring and SI cranks or has the 'upgrade' changed it to something else?  If so, I'd be put off. So your ultegra v 105 is probably shifters, brakes and rear derailleur. In which case the 105 if its the R7000 is probably going to be better (imo)  read some 105 R7000 reviews. For starters you'd think the 105 should have a bit more stopping power as it has bigger discs.

If I'm looking at the right versions of the bikes, the only parts on the older one I think are better are the wheels (which are still entry level can be had for about £200 in a sale) and original crankset if its still on. 

*If the BB shell is 68mm wide you can use adapters to fit shimano cranks, if its 73mm you can't - the shell width varies depending on the version.

I would suggest that 52/36-11/28 is not necessarily an upgrade (assuming the original set was Ultegra too), but more of a side-grade for different use circumstances. Depending on your fitness, local terrain and aspirations, it may be that 50/34-11/32 is a better fit for you.

Ultegra 6800 and 105 7000? Or 8000 and 5800? If the latter, would probably go with the 105. Was there a synapse frame update between  2016 and 2019 as well?