There's no proper way to please everyone when compiling a games list, but a suggestion would be to use metascore since it would be the simplest way to get an "Aggregated opinion" to try to please the most at first. This is what I recently did when trying to look up games for Nintendont via SD:
Metroid Prime, Resident Evil 4, Twilight Princess, Wind Waker, Soul Calibur 2, Viewtiful Joe, Eternal Darkness, Smash Bros Melee (Project M as well?), Mario Sunshine, Metroid Prime 2, Star Wars Rogue Squadron 2, Pikmin 2, Pikmin, & F-zero GX.
Would cover the ""Nintendo Exclusives"" that go on metascore from 89 to 100 and would certainly please a huge amount of people.
Super Monkey Ball 1 & 2, Animal Crossing, Paper Mario Thousand year door, Mario Kart Double Dash, Tales of Symphonia and Viewtiful Joe 2, Fire Emblem Path of radiance, Metal Gear Twin Snakes & Ikaruga get tons of praise as well, and would cover the "Nintendo exclusives" from 89 - 85.
That would be a decent way to start, then you could decide if it would be worth re-adding games that are already ported for other "platforms" (like wind waker and twilight princess which have been remasted) or postpone them until you get others out of the way; and then start adding some other popular favorites (Mario sports games).
Do you plan on adding more wii games as well? those that haven't/won't be released and are being done via injects?