Well Mario is obviously the official mascot of those games, he's the mascot of almost everything with the word 'Mario' in the title, but I personally see Waluigi as an unofficial mascot of those games because when I think of them I think 'Waluigi' and when I think of him of think of them. That's one of the reasons why he's grown on me over the years (I used to hate him). Another reason is that I agree with you in regards to him having a great and unique personality, his scenes are usually the funniest in the spin-off games because of his bizarre appearance and character. He's wacky, insane, petulant, over-confident, immature, a terrible sportsman and a joke villain character who probably isn't allowed within 200 metres of a nursery - I like that. Plus his ability to swim in the air is as awesome as it is nonsensical.
I think Nintendo have let opportunities for Waluigi in a major Mario/Wario/Luigi game slip by is mainly because of the amount of 'hate' he gets. I'd say it's more likely the latter than the former since they're known to decide what characters feature in a game or what characters get their own games based on the fan reception of that character. The prime example is Tingle: popular in Japan - his spin-off games get released there, unpopular in North America - his spin-off games aren't released there. I don't know what the feeling for Waluigi is in Japan, but in the West Waluigi has his fans but he seems to get much more bad press than positive.
Waluigi will probably never get his own official game, but he has got a fantastic looking fan game: