This thread at Digital Press was linked on MMN's forums. There's a ton of photos of Capcom internal images and memorandum, including some interesting looks at in-progress box art designs for several games, as well as story outlines.
Two such blurry letters can be found amongst them, related to Mega Man 3. I transcribed parts I could make out:
SUBJECT: Mega Man 3 Story
Here's the story:
After his defeat at the hands of Mega Man, Dr. Wily decided
to abandon his evil ways and devote his talents to another
joint effort with Dr. Right. Together they worked to build
Dr. Right's life dream, a giant robot called simply "8".
This robot, when completed, would be a major force in insur-
ing world peace. Finally, development was nearing comple-
tion and all taht was needed were the 8 energy elements
scattered among unexplored planets.
Without warning, the specialized mining robots on all 8
planets went crazy and rebelled. After tryin in vain to
regain control, Dr. Right had no choice but to send in his
best task force... Mega Man and his new dog Rush.
I am currently trying to find out more about the dog but he seems
to act as Mega Man's vehicle. There is one attached picture
showing Mega Man using Rush as a boat. I have requested pictures
of all Mega Man vehicles and weapons and should receive them in a
couple of days. The vehicle set will be complete but the list of
weapons has not been finalized yet so I will try to send those
piecemeal as I receive them.
If you have anymore questions or requests, I will do my best to
help out anyway I can.
P.S. Ducktales Game Boy has the same story as the NES version.
DATE: May 10, 1990
SUBJ: Mega Man 3 Items; Screen shots for MM3 and DT
+ Rush functions as a vehicle. He can fly and dive with Mega Man on top and can act as a catapult for Mega Man.
+ Mega Man can shoot normal shots while riding Rush.
+ Rush's base color is red as you will see in a color copy that should arrive in a couple of days. This color may change based on what vehicle he is acting as.
+ Rush was made by Dr. Right.
+ Needle Man (NE) - Needle Cannon
Continuous shot in the horizontal direction.
+ Magnet Man (MA) - Magnet Missile
Shoots horizontally. When it gets below an enemy, it Magnets in on them (actually, I think it just makes a 90 degree turn and flies up into them)
+ Gemini Man (GE) - Gemini Laser
Fires horizontally and deflects off walls at a 45 degree angle.
+ Hard Man (HA) - Hard Knuckle
Destroys certain walls (ala Crash Man of MM2)
+ Top Man (TO) - Top Spin
Mega Man's body spins and attacks enemy.
+ Snake Man (SN) - Search Snake
Crawls (quickly I presume) along a wall.
+ Spark Man (SP) - Spark Shock
Throw sparks at the enemy.
+ Shadow Man (SH) - Shadow Blade
Flies out in five directions (left, right, up, up/left, up/right) and returns.
Real screen shots still seem to be a problem. I guess they are drastically changing both games' backgrounds as I write.
Rush is merely a twinkle in ......'s eye at this point.
You guys.... this stuff is beyond cool.