Yes, superior equipment doesn't mean it will play better
many ports and subsequent releases include significant patches and fixes, especially in the earlier days. soukyuugurentai for the saturn - the original has some bugs that are fixed by the saturn collection edition, which also adds english support. is the original better?
The xbox port of Silent Hill 2 adds significant content, which was backported to PS2 in a greatest hits edition. Is the original superior?
Virtua Fighter 4 released on PS4, but a greatest hits version, Virtua Fighter 4 Evolution, includes game balancing, loads of features, and a 10th anniversary edition of Virtua Fighter. Is the original better?
Speaking of Virtua Fighter, the original Saturn port was so poorly put together, so maligned by fans, that Sega put out Virtua Fighter Remix, with better textures, a faster framerate, and all around better handling. Is the original Virtua Fighter the better game?
But though you didn't say it explicitly, I guess you probably mean a game on its original console is always better than a port to a newer console. Let's talk about that, then.
The first Valis game was released on MSX. It looks like this:
Is that better than the PCE release, which looks like this?
Is this game
Better than this one?
As much as I love Riviera on the Wonderswan, and has its specific charms related to resolution and colore palette, would you say the japanese-only wonderswan original is superior to playing it on GBA or PSP in English with extra content?
Even the lovely Panzer Dragoon. Is the Saturn version
Truly superior to the PS2 version, which just increases the fidelity of the textures?
I could go on forever, but original is not always best, and quite often the original can't fully execute the developers' desired vision.