It was developed mostly on Wii so even if they did upscale graphics how would they make larger worlds or many different Pikmin then previously intended? If they add a new Pikmin then originally planned then they have to reimagine everything to put those pikmin to use in puzzles & combat. The maps won't that huge or they once again have to start from scratch. If they did a complete HD makeover with all the extra stuff then it would take a few more years. So don't expect a Pikmin game that would blow you away. At least the graphics will look nice
This is Nintendo we're talking about. Many of Nintendo's developers especially Shigeru Miyamoto will throw out a game and start over if ideas and concepts added don't mesh with work already done. It wouldn't surprise me if development changed greatly after the decision to move the title from the Wii to the Wii U was decided. Pikmin 3 itself likely switched consoles during development when ideas and concepts the devs wanted to try couldn't be done on the Wii. Its not entirely impossible that because of the switch to Wii U that not only will there be more Pikmin on screen than was possible with Wii, but improved graphics and new concepts than were originally done for the title before switching platforms.