I disagree with anything over 20W needing to run new wire. I have at least 75W if not 150W RMS running to each speaker without issues, and my Kappas sound amazing. I have talked with more audio shops than I can count and they all told me it's not worth replacing the speaker wire from the center console to each speaker. The OE wires are sufficient to handle the power you need.
Good speakers have a capacitor to prevent alternator whine in the speakers. To avoid alternator whine, make sure you have a good ground on the amp (measure with multimeter). I have no issues with my setup whatsoever.
Here's my thoughts... Using an amp of 20 watts per channel... eh, upgrading the speaker wire is borderline. Me? I'd do it (probably) because I do overkill stuff, so I'd agree with Brian but it's not critical, if I'm honest in my opinion. The deal with factory wire and factory head units, vs. aftermarket... When the factory tells you 30wattsx4, it's really 5wattsx4. When an external amp tells you 20wattsx2, it's really 19wattsx2 (get my drift?). Upgrading the SPEAKER wire for 20x2 is ok, but not necessary. If you have an amp of 40 watts per channel, I'm upgrading speaker wires.
Now... 12V wires into the head unit... I'm reluctant to upgrade the input to the h/u. If I'm using h/u power, I'm already compromising my sound quality. Not only that, but if I care about sound, I've upgraded my speakers and I've probably upgraded my amp for the front channels. Therefore, my h/u is only running the rear speakers, and I don't care much about them. That's my viewpoint
As far as alternator whine... it can be due to grounding issues and it can be due to power wires run next to audio wires. In home installations, there are other problems, but I'm not going there now.
FYI, I'm drunk now, so I might take all this back tomorrow
** None of the opinions expressed in this thread are wrong. We are all aiming for a system built with money put towards the IDEAL place to increase appreciation of the listening experience. I make my recommendations based on saving money in certain areas, in order to put money into other areas that will have a greater impact in the final audio output quality.