All right, I'm gonna be the madlad who fires the first shot heard around the world cause it this point, we're reallyyyy dragging this out and no arguments have been made yet. Also, sorry in advance for being a Naruto pleb who doesn't know much at all but I'll try anyway. ALSO THIS IS LONG AF WARNING.
First off, Mega Man has a lot of advantages here. He's a High 6-C+ facing off against a High 7-A Obito who makes it to 6-C with the Biju so Mega Man already has a huge advantage in overall stats (except speed obviously cause it's equalized). Hell, Mega Man one-shots once he gets the chance and can tank a lot of Obito's attacks. Obito's regeneration isn't going to help with that big of a gap. Even if Mega Man gets damaged enough, he has Energy Tanks and can even call Eddie to drop him energy if he needs it (since it seems they're allowed).
Secondly, Mega Man is a robot so anything biological, spiritual, etc. isn't going to be affecting him at all here and he won't be influenced by chakra. Genjutsu, for example, won't work (as said in previous posts).
Now to address some previous posts in no particular order:
Substitution and clones overall are useful, but Mega Man can counter them with his AoE, homing attack and danmaku-esque attacks like Rain Flash (acid rain storm), Gravity Hold (increasing and reversing gravity in the area by 20 G), Power Stone, Crystal Eye, Dive Missile, etc. Also, Mega Man can answer Obito's speed boosts with abilities like Time Slow and the previously mentioned AoE weapons. Besides, Mega Man already has experienced being drastically outnumbered and being attacked from different directions before and so his experience and natural reflexes should do well here along with his acrobatic abilities like the slide. He also has several forcefield weapons to protect him. If anything, it sounds like trying to attack Mega Man (that's on top of his massive advantage in stats) would be frustrating just as much.
Mega Man having prior knowledge on Kamui is also a big plus. Knowing that's Obito's greatest trump card here, he's going to be conscious of it the whole time and utilize anything he can to prevent himself from getting the BFR. On top of what I said previously as well, it's going to be difficult and frustrating for Obito to tag him with it. The Biju are much stronger, but they're still noticeably weaker than Mega Man, who can just outright obliterate them. Also, if the Class T calc for Mega Man gets accepted as we're discussing this, he won't be restrained by Obito's chains. Even with Mega Man's current Class G, Mega Man still has means to escape such as his cutter Special Weapons (like Rolling Cutter, Metal Blade) to slice them off or can use other means like forcefields or general dodging to try and get them off of him. Hell, knowing the capabilities of Kamui and knowing that he has to escape, Mega Man can even teleport out of those sticky situations to prevent being tagged and BFR'd. And if Obito creates clones of Mega Man, it wouldn't be too surprising since he has fought several clones of himself before and has the means to take them down.
Additionally, Obito knowing about Time Stopper is a problem, but that's not Mega Man's only win-con nor is it something he desperately needs to rely on unlike Obito and Kamui. Also, there's still room for error on Obito's part. Time Stopper gives Mega Man a purple and white appearance which may help Obito know that he's gonna use it, but the problem is that other weapons have the same color scheme. Flash Stopper and Time Slow have very similar or the exact same colors so Obito can be tricked here into thinking Mega Man is using one move when it's actually another. Marginal, but could help. On top of that, Obito's intangibility lasts for a few minutes before he needs to recharge and Obito can't use both intangibility and teleportation so he's vulnerable when he switches (correct me if I'm wrong) which gives Mega Man windows of opportunity to hit him.
OKAY, that was long, but I vote Mega Man due to having his robotic physiology (so he won't be effected by anything spiritual or biological), a massive advantage in overall stats (meaning he can take a lot of punishment and obliterate any distractions while also making it so Obito can't man fight him), having the versatility to answer a lot of the problems Obito may cause, having hax other than Time Stop (like Time Slow, Flash Stopper (to blind and stun), Gravity Hold (to screw with gravity and BFR), Attack Reflection (to combat Obito's own), etc.) and prior knowledge on Kamui which would make it more difficult for Mega Man to get hit. I just see Mega Man having more success so far, but this is very close.
Again, if I got anything really wrong or am misinformed please let me know cause this is a hard ass match up as it is.