Okay, I didn't want to have to post this, since as most technical things come I am able to solve them myself, eventually... 
Anyway getting straight to the point: Since the first game I was trying to run was Resident Evil's rail shooters, I had to use a Wiimote, and I don't have any I decided to use my USB Logitech RumblePad 2 controller and keyboard/mouse.
When I use the original Wiimote plugin (the one that comes with 'official release') I can't use my controller to play the game, I can set the controls in the options menu, but when I get in game no controller button works.
Additionally I tried the Incomplete Wiimote Plugin (the one that comes with the latest SVN build on dolphin-emulator) but that one didn't even recognize my mouse input ingame.
I'll post a picture of my wiimote plugin settings if required, until then I'm gonna keep trying different settings and revisions.
tl;dr Neither wiimote plugin works.
SPECS:
Windows 7 x64 Ultimate
Intel i7 860 2.8ghz
AMD Radeon HD 5850
8gb Memory
USB Logitech RumblePad 2 (plugged in to a USB2 slot, can be plugged in to a USB3 slot if required)
Generic Microsoft Keyboard and Mouse
Dolphin Official 2.0 and
Dolphin r6214

Anyway getting straight to the point: Since the first game I was trying to run was Resident Evil's rail shooters, I had to use a Wiimote, and I don't have any I decided to use my USB Logitech RumblePad 2 controller and keyboard/mouse.
When I use the original Wiimote plugin (the one that comes with 'official release') I can't use my controller to play the game, I can set the controls in the options menu, but when I get in game no controller button works.
Additionally I tried the Incomplete Wiimote Plugin (the one that comes with the latest SVN build on dolphin-emulator) but that one didn't even recognize my mouse input ingame.
I'll post a picture of my wiimote plugin settings if required, until then I'm gonna keep trying different settings and revisions.
tl;dr Neither wiimote plugin works.
SPECS:
Windows 7 x64 Ultimate
Intel i7 860 2.8ghz
AMD Radeon HD 5850
8gb Memory
USB Logitech RumblePad 2 (plugged in to a USB2 slot, can be plugged in to a USB3 slot if required)
Generic Microsoft Keyboard and Mouse
Dolphin Official 2.0 and
Dolphin r6214