So I've heard that the WiiU system transfer transfers ALL Wii games and it's a one time process. However there are some games like Sonic Colors and Brawl which I love using the Gamecube controller for. Can I select which games get transferred?

no you cant select what u want. Its all or nothing

For Wii games, aren't you able to just save or copy the data to an SD card and put that into the WiiU?

You could, but I expect both of the games he's talking about have online data and on the Wii those kinds of save files cannot be copied except via the Wii-Wii U transfer software, so he can't simply shift them elsewhere.

only the software provided for free by nintendo will bypass any limitations your data may have preventing you from copying them

No.

When I did the Wii to Wii U Transfer, only the data on the actual Wii console itself was transferred to the Wii U, not the stuff I had on my Wii SD card. I tried putting my old SD card in the Wii U after I did the transfer but despite recognising the data/VC/WiiWare games on it, the Wii U wouldn't run any of them. I had to go on the Wii Shop Channel (via the Wii U) and redownload all my games all over again.

This was especially annoying as when I bought a 3DS XL earlier in the year and transferred the account from my old 3DS onto the 3DS XL, all I had to do was put my old SD card straight into the 3DS XL afterwards and all my E-Shop downloads still worked.