I think OP's basic premise is mistaken (Here are about 5,700 results from Google Books for "I have wanted to ask", so it's certainly not true that we never say it.
And in some contexts ("I've always wanted to ask", or "I have wanted to ask for some time now"), Present Perfect is arguably more natural than Simple Past "I wanted to ask".
As OP suspects (and as backed up by his comment re 2,120,000 GB hits for "I wanted to ask"), the Simple Past form superficially seems almost 40 times more common.
Whilst I agree Present Perfect really is less common than Simple Past in OP's "polite question" contexts, the preference is nowhere near as marked as those figures suggest, since most of the 2,120,000 instances reference past time in a "narrative" context (where only Simple Past works).
But even allowing for that, I'm sure there's still a preference. I don't disagree with Barrie's point about Past Perfect Continuous (I have been wanting to ask) often displacing Present Perfect (I have wanted to ask), but there's at least one other factor in play here...
Both Past Perfect Continuous and Present Perfect imply strong links to the present moment. But in OP's primary context, "I wanted to ask [you] [some question] is often just a fairly meaningless "deferential introduction to an interruption" (a bit like the polite throat-clearing "Ahem...").
In such situations, the speaker is deliberately trying to create "distance" between himself/his words and the "present moment" (that's why we say "I wanted to ask" rather than "I want to ask" in the first place!). Obviously it would be counter-productive to use a verb form that's specifically adapted to linking events in the past to the present moment.
When you are speaking to your mother, you cannot speak as in strict prose or grammar, rather a statement in a document. It should be simple. I prefer banana over apple, which I would prefer over orange etc.
Best Answer
It doesn't sound unnatural to me at all, although the simple present tense might be more appropriate than the present perfect if the question was posed in the present tense (which suggests that you might still be feeling regret up to the present moment):
The present perfect is better if the question was posed in the past tense: