Hey, this is the author of Mega Robot Laboratory. Sorry I didn't respond sooner (check your PMs on board2, although some of it's redundant now with this post here).
The only Data in Wily Wars that's Compressed so far that I've seen (and I've looked through absolutely almost all of the data in the game), are some of the Level Art.
The Sprite Graphics therefore are all Uncompressed. The reason Protoman's Graphic Tiles look a bit messed up, and merged into other Tiles, is because the Data doesn't always start at an address ending in 0x******00, or multiples of 0x20 (each Genesis 8x8 Tile is 0x20 / 32 Bytes in size). To view/edit it properly in a Tile Editor, you'll need a program like YY-CHR, which can shift the starting address that it's viewing Tiles at by 1 Byte or whatever amount (since Tile Layer Pro can't do this, a lot of the Graphic Tiles you're seeing with that program are being viewed starting from somewhere in the middle of them, etc.).
To view the Graphic Tiles with the proper Palette (most Sprites have a different Palette, the ones that don't are mostly the ones that use Megaman's Palette, such as 1ups, ? Blocks, Energy Tanks, Plasma shot, Boss Doors, etc.), you'll need to edit the Palette in the Tile Editor to match the Palette of the Sprite you are Viewing. To see what the Sprite's Palette is, go to it in-game and while that Sprite is on-screen, and if using Gens, go to the Menu Option: CPU -> Debug -> Genesis VDP; if using Regen Debugger (an Emulator with extra Debugging options), go to Menu Option: Tools -> VDP Debugger. Once you create the Palette in the Tile Editor, be sure to save it so you don't have to recreate it the next time you use the program (I can't find an Import option of any kind, other than to load a Palette in some specific Palette format... a '.pal file').
If you need or want to make Protoman graphically larger than he is (add/remove Tiles to him), I can help you change his Sprite Mappings, plus his Collision / Hit Box size. I can also help you change his Palette as well if you want to do that for any reason.
Also when it comes to that Red Screen of Death stuff that you see when you try to modify the Game, it's due to a Security Checksum that the game has built into it to make it harder to modify the data. This is not the Checksum that each Genesis / Mega Drive game has in its header, it's a Checksum that this specific game has programmed into it. My Editor allow you to remove this. In my Editor, after opening your game, go into Edit -> Miscellaneous Data, and change the Region or whatever in there, and then hit apply, and then File -> Save Game of course. Right now I don't give the option to individually apply the SRAM patch or not (the game normally save in EEPROM format, which is not supported by Emulators, or most?), it will just auto apply with the Security Removal Patch (I haven't yet separated the programming of the Security Removal from the SRAM, as it's copied data from the below SRAM Patch; in other words I got a little lazy on that before, because it's pretty easy to separate them).
Here's also the SRAM IPS Patch (changes game save type from EEPROM to SRAM, removes the Security Checksum stuff, and changes the Region to USA).
Apply to a European .bin format Wily Wars game
http://www.romhacking.net/hacks/514/If you need a Program to convert SMD format ROMs to BIN, here's one:
http://www.zophar.net/utilities/segautil/sbwin.htmlHere's a link to my Editor also (it can only edit a little so far; it's mostly just for viewing Data as of right now, but I will update it / add features as I have time to):
http://acmlm.kafuka.org/uploader/get.php?id=4985And let me know if you need help with anything else

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------------- Here is a list of which Level Graphics are Uncompressed in the Game (all the other Levels have Compressed Gfx), just for your info if you care to know ---------------
~ Megaman 1 (All Compressed) ~
None!

~ Megaman 2 ~
Air Man
Wily Castle 2
Wily Castle 3
Wily Castle 4
Wily Castle 5
~ Megaman 3 ~
Hard Man
Gemini Man
Magnet Man
Shadow Man
Doc Gemini Man
Doc Shadow Man
Breakman
Wily Castle 5
Wily Castle 6
~ Wily Tower (All Uncompressed) ~
Buster Rod G
Mega Water S
Hyper Storm H
Wily Castle 1
Wily Castle 2
Wily Castle 3
Wily Castle 4