It has just 3 gears. Is your riding fairly flat? I don't know if it's the case with that one, but fixing a puncture on a hub wheel can be difficult, may not be ideal if pressed for time on a commuter.
Three gears can be fine: top for flat/downhill, normal for uphill and low for serious uphill... and above 15%, I'm walking but may be doing that anyway. Fixing a puncture on a hub wheel isn't too hard and if pressed for time, remove the sharp object from the tyre and dump a sealant canister in. You can't do the current fad of swapping inner tubes as easily, but that's an expensive approach to punctures anyway.
12.5kg is pretty heavy for a simple bike.
I never had you pegged as a weight weenie!
Tyres are not a reason to choose a bike, they are easy and often cheap to replace (they are a consumable). I think 40mm is overly fat for a bike used on the road, but personal preference [...]
I think 37mm is a fairly common road-going tyre size (it's near enough that it was sold as the old 1⅜" as in 28x1⅝x1⅜" and 26x1⅜", as well as the c in 700c when 700 was the tyre diameter and c indicated the width) and some tyres listed as 40mm are closer to 37... and most such tyres are run closer to a comfortable 60psi than the filling-rattling 110psi used by many racier road bikes now... but ultimately, yes, tyres are relatively cheap and it's usually easy to vary tyre width by a few millimetres.