That's probably because the Metal Gear Ray he's fighting here is different from the 20 that he went up against on Arsenal Gear. Those 20 were mass-produced AI-controlled units based off the Navy's first prototype shown on the tanker.
There's bound to have been some improvements since then. Consider the Metal Gear Ray fight in MGS4, it took Snake piloting Metal Gear Rex to take it down and it wasn't as simple as a few rockets to the mouth like in MGS2, though it's possible Ocelot piloting it may have had something to do with that.
This one in MGR is a custom version Ray that's probably been modded to be even more powerful than the one in MGS4. If Raiden's having a harder time then it's only natural. Though still even managing to go toe to toe with one as he presently is god damn incredible.
