Actually, X was not built with the intention of being a war machine. Light had hoped that X would not have to fight, actually. Remember in X1, when you come across the first upgrade capsule, Dr. Light says this. However, Light also planned ahead and made him very capable of being a war machine, just in case.
Now as for who I think would win, Mega Man X or Mega Man? I think X would win by a long shot. First off, lets look at their general combat capabilites. (Assuming we're taking them from strictly the games, and not cut scenes and anime sequences.) Mega Man can jump, climb ladders, shoot, charge up his Mega Blaster, aquire weapons, and slide. That is the most upgraded version of Mega Man. The most upgraded version of X can jump, dash, air dash, climb walls, dash jump, climb ladders, copy weapons, charge up his X buster to levels far beyond a mega blast, and charge his copied weapons. X also has the capability to be upgraded further with armors. Mega Man did have the capability to use Rush as armor, Power Mega Man, and Jet Mega Man to be precise, but honestly even with those and Beat do you think that would be a match for X in the Golden Armor, or Ultimate Armor for that matter? Then lets get technical, X's "CPU" if you will, is far...FAR more powerful than Mega Man's. His tech specs listed in X1 are way...WAY more advanced than Mega Man's. Of course just look at processor advancment today, CPUs 5 years ago can't even begin to compare to CPUs today, and it's obvious that this isn't differnet in Mega Man and X's world. There is also a much greater time span than 5 years diffence at play here... X also has one other ability that the original did not, and completly free will. If Mega Man had that, Light would not made a big deal of it in the beginning of X1 in the warning. So...X is better technolgically and capabilitiy wise, so that leaves skill if you will? Well if you look at all of the Mavericks X has fought and compared them to all of the creations of Dr. Wily Mega Man has fought, which are more powerful and complicated? The Mavericks, of course. X has shown the capability to beat things far more advanced them himself just as Mega Man did. However, this means a lot more in X's case, because in the end he's fighting things that are more than a hundred years ahead of him technology wise. Mega Mtan hasn't done that has he? Although its not really clear how advanced the robots in Mega Man V are in comparison to Mega Man, but I just can't seem them being as advanced comparison to the ones X fought at the end. SO therefore my logical conclusion is that X would HAVE to win in a fight against Mega Man. Unless Mega Man managed to win by sheer luck somehow...which is besides the point in my opinion.

Light designed X to defend peace, and originally equipped him for war, knowing that that would come.

Not exactly, Light had originally hoped that X would not have to fight. He didn't just give him all of his armors and upgrades to begin with because of this. He had hoped X might be able to lead a "normal" life, and be more human-like. That was his original intentions anyway. He also prepared him for alternatives, thus the upgradability. Of course, compared to how the original Mega Man started out, X looks like a war machine, but that really wasn't supposed to be his purpose in life. If that had been the case, do think Dr. Light would have given him the capability to worry? If he had been built to be a war machine, he probably wouldn't have.

Yeah, those alternatives... kinda what I was talking about. Yay loopholes!

If Light had not had some inkling of X needing to be war-equipped, why did he seal him with powerful armor, a souped-up MegaBuster, and a store of new abilities pretty much useless to a normal human?

I never said that Light didn't think that X would need to be prepared to defend himself, I just said that Light didn't want X to be a war machine. It's just the way it worked out, and Light obviously knew that it was pretty hopeless to hope that it wouldn't turn out that way. I mean, you can't have mankind, or man-like robots for that matter, without war can you?

And technically he DID store him with a suped-up Mega Buster. Remember, for Light's day and age, the X-Buster was the most advanced weapon ever created, utilizing plasma energy instead of solar energy.

He probably designed all of X's armor and upgrades AFTER he completed and sealed X away.

There's no doubting either one of your points here.

Thanks for the compliment!

I think that's a pretty good point, Mega Man and X would never fight each other to begin with. It would have to be an extraordinary event if they did, perhaps X going Maverick or Mega Man being under Dr. Wily's control or somthing.

Maybe Mega would go maverick. I mean, if the virus can infect simple mechaniloids...

Hey, it infected Doppler!

It's possible for them to fight. I mean, look at Mega Man and Quint. Anything's possible.

No it's not possible, Megaman was turned into a toaster.