I'm not talking about parallax. I'm talking about everything else BUT parallax. Ditch the 923487 layers of parallax, and there's NOTHING in that game that couldn't be done on the PCE.
Well now that you put it that way then yes, you're absolutely correct...
Shovel Knight was designed by tech experts who did a lot of research to determine exactly what kind of accelerator chips NES games would use in the future and made the game fit within the technical limits of the NES hardware with those chips.
Just physically port over those chips into the Shovel Knight HuCard and quintuple the parallax found in the computer version.
If we got to the point of actually putting Shovel Knight on a real NES cartridge, then pretty much the whole hardware would be inside of the cartridge and the NES itself would only serve to power the cartridge, provide input and MAYBE use the soundchip...
Heck I doubt it would even be able to output an image, the cart would most likely have an HDMI output in it somewhere and you'd connect the cartridge to your TV, not the actual NES...
I mean seriously, not only does the game have countless background layers, it also completely breaks the NES's colour count per sprite/tile and colour palette (Like, seriously, the game uses a few colours that aren't even on the system's palette) and it does gigantic well-animated sprites, has NO flickering what-so-ever, uses an extra soundchip for audio AND plays sound effects without clipping ANY of the sound channels on top of that, not to mention the game displays exclusively in widescreen! There are NO 4:3 options...
At that point, even if the game is on an NES cartridge, is it even an NES game still? I'd say the point where it stops being an NES game and starts being something else is the moment when you're outputting the image from the cartridge to the TV, and not from the NES...
Putting all of that extra hardware on the NES cartridge would be no problem because the thing is as big as an aircraft carrier, meanwhile all the PCE would need would be 2 or 3 extra sound channels (2 for no loss in musical detail, 3 for no sound-clipping, preferably one of them would be an ADPCM to mimic the NES DPCM without any wasted CPU cycles by playing a sample on a PSG channel) about a million extra BG layers, maybe one extra sprite layer too in order to avoid flickering (not like it would be likely on the PCE but better safe than sorry!) and some way to support a widescreen display... That's about it really... If you could cram the necessary hardware to pull that off on a HuCard then great! A 1:1 port would be pretty much a matter of actually going and making it, but personally, I'd rather just use the base hardware and push it to the limits, that's why I said a side-game with the same gameplay, but better graphics, re-arranged (read "better") music, similar level design, but all optimised for the PC engine would be a better idea than attempting a straight port of the game...