I find it amusing a brand new car only gets 3 MPG more than cars got 50 years ago... With no overdrive.
I'm not VW expert but the concepts are the same for all engines. For more MPG you can take a few approaches. Not sure what kind of exhaust is on it but start with a good flowing header, eliminate catalytic converter or replace with a higher flow one, stick with a quiet but good flowing muffler (for your application any old long case turbo muffler will be slightly louder than stock but still very quiet).
As for intake, I would be surprised if anyone makes intake manifolds for those engines, though you seem to indicate they do. Any offerings will likely hurt MPG as factory intakes are typically pretty good for lower RPM torque at stock displacement. Wasted money I think, without knowing specifics.
Ideally you should be at least port matching intake and exhaust ports if changing intake manifold or header. Not sure on VW port design but there is probably some efficiency to be had with working the short turn and bowls, as there are on most as cast factory heads. Upping the compression to run 91+ octane will also help MPG. Polish the chambers for added detonation resistance and if it has a quench pad in the chamber consider adding Singh grooves for even more detonation resistance. Compression is key to getting excellent MPG.
If you go to that extent you should be making more lower RPM torque and can probably change gearing to drop a few hundred RPM at highway cruise. No reason a modern econobox like that should be getting 45+ MPG.
Alternatively, accept that you bought a new car and it is what it is. Remind yourself to shift and you're golden.