As I was hacking around last night, I discovered the same thing. My current thinking on the matter is to alter the enemy sprite handling routines to use a second table if the enemy ID is above a given number. As the new enemies are all likely to have IDs higher than the existing ones, it should work nicely.
I know why the Gooba sprite tile that's simply a mirror image was done that way, rather than by reusing the other tile. The game has a horizontal flip routine that doesn't play nice with mirrored tiles. Mostly it's used for enemies (and Mario) when they are moving or facing to the right. However, it's also used by the special cased Goomba animation routine, even though the Goomba keeps moving left.
The horizontal flip routine works by swapping the left and right tiles and then enabling the horizontal flip attribute on them. This means that if you've set the horizontal flip attribute of an individual tile, if the sprite is modified by the routine, the results do not turn out correctly.
The only enemy in the game that has mirrored tiles and faces both directions is Lakitu and they avoided the issue in his case by not using the horizontal flip routine, but instead by handling it with a special case in the general enemy mirroring code.
It'd be tempting to just restore the Goomba tile and find another one to use, but it's not the best solution. For starters, the barrel is going to need to be treated similarly due to it's mirrored tile. Plus, the Fighter Fly, with one animation frame mirrored and the other not, is going to need to be handled.
The solution I'm pursing is to turn the Goomba from a single frame into two frames and handle the mirroring in a special case like they did with Lakitu. However, I've yet to figure out how to determin which frame the enemy is on when the mirroring routine is called. The Lakitu code isn't any help here as it does it's frame and direction determination based on stuff that has to do with enemy frenzy and the Spiny throwing.
I'm confident that it can be done, but I've yet to figure out exactly how yet. Until I do, I can't really fully impliment the graphics additions. However, it's nice to see that you've got the levels edited and ready for when I get the power-up graphics inserted.
Do you think I should release an expanded ROM with the placeholder graphics like I did with the 1-4 patch? Or should I wait until the power-ups have graphics of thier own?