Actually it's pretty well established why Zero wouldn't have been around in X1 to obtain the armor upgrades. Immediately after the Intro level X and Zero split up. Zero tells X that while X is hunting down the mavericks he would be scouting Sigma's HQ for information. They then meet up only once more before Zero is blown to bits. In X2 Zero is a scrap heap until the very absolute final scenes in the game. Again, this is why Dr. Cain makes the perfect choice for the capsules... as Dr. Cain was the one who rebuilt Zero. On that note, however, Zero himself (as I recall) says to X he is still not fully functional and that is used as an explanation as to why he gets just 1 life.
Might be best to set the game in an alternate universe, one where Dr. Cain learned from his mistakes with the reploids, but was already fired from the company producing them (to explain why there still are mavericks), and is thus better able to figure Zero out. I still really do not like the idea of Light giving him armor upgrades. The capsules made by Dr. Light were made purely to oversee 30 year boot-up, and debugging sequence X had to undergo before being activated, as Dr. Light was afraid that X would run wild and do harm to humans as he was the first robot that did not have to follow the three rules of robotics.
It makes sense that Dr. Light built into those capsules a way to modify X on the fly or even had already produced his upgrades with the intent on slowly giving them to X as he proves his worth to humanity. I know if I made a robot that might go on a killing spree and take out a city I wouldn't fit him with his best armor and weapons right out the gate. Although should you do decide to use Dr. Light here's what I came up with.
DR.LIGHT - What's this? You are not X, this shouldn't have happened. A malfunction maybe?
ZERO - Your face, it seems almost familiar somehow... I kno--
DR.LIGHT - !!! Oh dear, that signature, you finally managed it... Wily. Did you ever learn, I wonder.
ZERO - You know me?
DR.LIGHT - Oh, yes, almost certainly. It seems like you've had a rough life. Fractures on the casing, poor soldering, even a mixing of alloys. I wonder what you've been through. But I'm getting ahead of myself, tell me, have you encountered a robot named X?
ZERO - You know X too!? Who are you!? Tell me now!
DR.LIGHT - Yes, that seems about right. That anger seems forced though, never learned after all Wily?
ZERO - Wily? You keep saying that. Who are you!? Who is Wily!? If you are trying to harm X I won't allow it!
DR.LIGHT - Do not worry, uh...
ZERO - Zero.
DR.LIGHT- Zero. I am Dr. Light. I created X. I'm starting to get the picture. Ah, and just in time.
ZERO - You CREATED X? gah.... my head, it... who. Wily?
DR.LIGHT - Oh dear... Zero, pay attention. I've scanned your systems and I can see a lot of room for improvement. I can repair you to full functionality, if you would do me but one favor.
ZERO - ...
DR.LIGHT - Keep watch over X. I'll tell you more about yourself in return, or at least all that I can.
ZERO - ... I promise.
DR.LIGHT - Fantastic! [insert upgrade 1 here]
It's a rough idea so far, but basically I see that as a way for Light to ensure that Zero is more stable and under his control. When Light scans Zero he sees something in him, a signature design piece that all of Wily's creations have had in the past but at the same time his programming is like X's. It has free will. This also builds up the foundation for Zero's dreams about Wily. I don't think Wily would trust Zero totally though, and what information Zero in check. To possibly even paint Wily as a hero to allow Zero to act more noble. It's a work in progress, hopefully you can use Dr. Cain.