A new version was recently released (the download was taken for a while earlier but it's back now)! Here's a copy of the changelist from his site's forums:
Knockback has been reduced and can be adjusted.
The player can slide cancel when direction is changed.
The time to charge up a shot has been reduced.
The player can choose how spikes will damage Mega Man.
A new save file system has been implemented.
The new save system allows for saving between the final stages.
The number of checkpoints can be changed by the player.
The default controls have been changed.
The stage select cursor now begins on Mega Manís portrait.
Less enemies will explode upon defeat.
Mega Man no longer gets stuck when damaged in slide paths.
Mega Man recovers 10 bars from large energies rather than 8.
Pausing will place the cursor on the weapon Mega Man was last using.
The intro scene will replay once the title screen music has finished and no player input is detected.
Mega Man can detach from ladders more quickly.
Minor alterations have been made to the ending dialogue.
Informational screens and most cutscenes can be skipped.
Mega Man can now fire more rapidly.
Deflected shots will clear the screen more quickly.
Mega Manís hit box has been modified.
Most enemy and obstacle hit boxes have also been modified.
Mega Man detaches from ladders much lower than before.
He can also grab ladders further above his head.
The charge shot will not continue to charge while sliding.
Some levels have had minor alterations.
The strength of Mega Manís slide ability can be adjusted.
The duration of Mega Manís recovery period can be adjusted.
Bug Fixes: *Spoilers*
The pause screen glitch preventing input from the player has been fixed.
Terror Man can only summon a finite number of buggers.
Terror Man cannot be defeated off screen.
The electrified water will destroy Mega Manís clone rather than damage Mega Man.
A similar modification has been made to the shock tiles.
The electrified water will not send Mega Man into the ceiling.
Rash blocks (snake platforms) will not send Mega Man into the wall.
Mega Manís clone will lower on the coffin with the player.
Spikes will squash the player to death in Death Manís stage.
Volcanoid and Chilbert no longer react to player weapons.
The player can no longer pause during transport.
The music wonít stop when the game is paused.
The charge shot no longer stops invincibility frame flashing.
Rush Coil no longer refills when the weapon swap is used.
Deflected shots will not make multiple *ding* sounds.
Mega Man cannot detach from ladders while climbing.
Items no longer pass through spikes and other platforms.
Mega Man will not stop firing on a ladder if the fire button is pressed too rapidly.
Utilities should not spawn in walls.
Pit Pods will not explode when regenerating in a pit.
Tube Tank barriers will not glitch the player into a wall.
Mega Man reliably attaches to ladders he is closest to.
Mega Man will not turn invisible if his recovery period ends while sliding.
Robot Masters will align to the proper Y-coordinate when Mega Man enters the boss chamber.