Wait, you have Mother 3, a game you have to pirate to play in there but no Ninja Five-O? At least NFO can be bought legally and played.
Seriously, disqualify Mother 3, you can't legally get that game and play it in English.
If you want a game you can reasonably get take Boktai 1 or 2 (that had TONS of surplus stock in stores here so it should be easy to find cheaply), since most people haven't played that it'd probably be something interesting and new to delve into.
I want to respond to all three of your points. First, Ninja Five-O is prohibitively expensive to acquire in cartridge form, and as an action game, it is not well-suited for emulators. Otherwise, it would be the perfect game for RetroActive, but I have to consider availability.
Second, it is legal to import Mother 3 from Japan, and it is almost certainly legal to hack your own copy with an English translation patch, or else play through the game using a translation guide. Yes, I am aware that most people will not go to that much trouble and will take the easier route of piracy. While I do not condone any kind of piracy in general, I personally would not feel guilty about playing Mother 3 via emulation considering it has never been released outside Japan. If Nintendo ever releases it in the West, I will be first in line (well maybe second, after the Starmen fanatics) to pay for my own copy in English. We have seen no indication whatsoever that Nintendo has any intention of doing so. If my choice is between emulating a game or never playing it at all, I am willing to consider the former as a special case. I thought there might be enough RFN listeners who agree that it would be worthwhile including Mother 3 on this list. Of course, some people will disagree, and you are free to express that opinion through your vote as well as here in the comments. But I will not disqualify it from the poll. You are factually incorrect on these three key statements: you do NOT have to pirate the game, you CAN legally acquire the game, and you CAN legally play it in English.
On the subject of Boktai, I have long planned to include Lunar Knights in the DS poll and thus chose to omit its predecessors from the GBA poll.