I look away just for a day, and now I come back to find two excellent versions of the logo! Thanks to both of you!
I think my imaginary ideal version sits somewhere between the two. Since you're going for authenticity here, I think it's great to have it match the official version from the GBA release as close as possible. However I would take a good thing that was achieved by SuxMenner by making it from scratch, simplicity of shapes and outlines, and apply it to the official one.
Maybe you're already considering what I'm gonna suggest now. Similarly to what I suggested for your Mega Man X logo, I think the transition to smaller resolution needs to shave off some of the outlines the higher resolution logo has.
Something I immediately noticed when comparing both version is the inner white outline on the official one. On a smaller resolution, I think it looks way better without it.
(Sorry for hacking on top of your work, I made this on a hurry to make my point. It's not respecting palette color numbers either.)
It would make it a bit closer to how the japanese in-game logo looks like too.
In fact, now that you already have the shapes and outlines from the downscaled american logo... From now on, I'd suggest you take the in-game japanese logo as a reference for any further decision on manual tweakings (palette and color adjustments, outlines, antialiasing, shadows)
Speaking of palette limits, you already know the drill and wisely considered it from the start. But I don't think SuxMenner did? (I tought it looked a bit too soft on the borders. Photoshop indexing is reading 42 colors from it)
Unfortunately, until someone hacks it into the game and confirms of the logo is actually composed (layers, palettes), we're just making guesses. My guess (and I repeat, GUESS) is that the graphics are all on the same layer, but it has at least two different sets of palettes, set depending on the tile.
Wow! I'm amazed someone worked a new logo into the game ALREADY! It certainly is an improvement over the one on the first post! However, since the source pic surpases palette limitations, it clearly suffered some compromises when inserted into the game. It has the same issues the one from the original post had, unbalanced color contrast and jagged outlines.
I wish we had the information he has on graphics/palette locations, and how the palette(s) are composed!