There are a lot of reasons, ranging from lack of quality, lack of advertising, failure to market to the correct or total demographic, and lack of an extended demographic to name of few.
Basically, Nintendo makes good games. Some are great, and some are just good, while only a few are below par (Donkey Kong Barrel game, I'm looking at you). Not everyone might like their games (WiiMusic), because they are not in the targeted demographic, but they are quality games nonetheless. Nintendo also advertises many of their games, and they are really good at advertising to the correct crowd (minus that WiiMusic E3 screw up), and many of their games cater to many different demographics, like Mario Kart. These things combined result in high sales for many of their games.
Take out one of these factors, and sales fall, with each factor removed sales falling further. Release a sucky game or a lame port? Potential sales fall. If you don't market your product, potential sales drop, though word of mouth has helped a lot of Wii games. Market a game like Boom Blox to only 8-12 year olds, though many other demographics could/would enjoy it? Yeah, you are loosing potential sales (thank goodness for word of mouth though...). Make a niche title? Get ready for smaller potential sales. That's just how it is. Nintendo is great at making their games fun for everyone, so many of their games are juts always going to outsell 3rd party games because 3rd parties are just not as good in that regard.
I've made a post about this a while ago. Here's a link.
But this is a good post from that thread that basically sums things up:
Ok so me and this guy are racing at the track. I'm hitting 220 mph on the straights. He topped out at 190 mph.
Pop quiz, hot shots. Is 190 mph slow? Does the fact I hit 220 mph nullify an significance of him hitting 190 mph? If you could take your car and do 190 mph, would that be fast for you?
Now for the analogy to work you have to replace me with Nintendo and him with 3rd parties. Then replace our speeds with their sales numbers.
Nintendo selling at X level doesn't mean the Y level of sales of 3rd parties is bad.
End of debate
