To start, Doom Guy have the AP advantage, by not too much. The thing is that Doomguy can really make the difference higher with the Quad Damage Sphere.
Porygon can make things work for him using Thunder Wave to slow Doomguy even with his speed enhancement on, boost his defense with Barrier and his speed with Agility. The holograms might be counter by the fact that Porygon normally will attack the one with low HP. Porygon also have alot of reliable recovery that is boosted by his IQ skill, plus the addition of passive recovery and higher HP. Conversion 2 will maybe help here, making Porygon resist to alot of Doomguy's arsenal and even immune to his Lightining Gun. Zap Cannon itself is a really powerfull move, that will land a hit if Lock-On is activated, Invisibility can also be countered by Lock-On, or the omni-directional attack Discharge. While Porygon don't have the incredible Nasty Plot, Charge Beam can be good if he have luck, while Sharpen can really boost Porygon's attack, but that will not be used to much, since Download will Amp his Special Attack, and only 3 moves benefit form Sharpen (Quick Attack, Tackle and Zen Headbutt), who each, besides Quick Attack, have better versions on the special side, and Doomguy can easily launch Porygon to the other side, via that sweet Class M.
But overall, while Porygon have some good things in his favor, mainly paralysis, recover and Conversion 2. I think that Doomguy might take this one, well, depending on some things, first of all, he can use all of his sphere things together, if yes, than this is prob a stomp, since his Invulnerability makes Porygon unable to damage him, if no, than the Invulnerability Sphere has a timer? If no, than Doomguy takes this on. If yes, i might need to rethink somethings to see if Porygon can make this, not voting till this is answered