An eBay user going by the alias of “dpstockboy7btb” has created a rather unique custom Amiibo. He or she was able to completely replace the Luigi figure with Waluigi. Moreover, the packaging was also modified to reflect the changes made to the statue. You can take a look at the fan-made figurine below this paragraph. While the top side has been completely replaced, the Amiibo still functions as Luigi. Therefore, you can only train the Luigi figure player when using the custom figure in Super Smash Bros. for Wii U.
Unfortunately, it seems somewhat unlikely that Nintendo will be releasing an official Waluigi Amiibo anytime soon. Nintendo is currently focus on the playable characters from the above-mentioned Super Smash Bros. for Wii U. You can take a look at the announced Amiibos so far with this page from Amazon.
With that said, Waluigi could end up getting one with the release of Mario Party 10 (and maybe even the next Mario Tennis game, if it does come out for the Wii U). He can also be played in Mario Kart 8, so there are plenty of opportunities for Nintendo to release a figure based on his likeness in the future.