AmEng speakers do NOT use definite articles all the time; whether we do or not depends on what we want to say, and how we want to sound saying it. In particular, the use of the definite article with the present tense of the verb "to be" depends (in the words of a famous American) on what your definition of "is" is. Several of your example sentences sound distinctly unnatural to my USAite ear. Here are my suggestions based on my own usage:
School:
- He is in school. - He is a student; specific time does not matter. Perhaps it's Friday night and he's partying right now.
- He is in the school. - This does not sound natural at all to an American ear.
- He is enrolled in the school. - He is a student.
- He is at school. - He might be a student OR a teacher, but he is on the premises at this moment.
- He is at the school. - "The school" is a local landmark, and he's there right now.
Hospital:
He is in hospital. - He's an inpatient. This is valid, but not usual American usage. Anglophiles (Americans who like to drop Briticisms into their speech to appear more sophisticated) will sometimes use this.
He is in the hospital. - He's an inpatient.
He is at hospital. - We don't say this.
He is at the hospital. - He might be an outpatient, or he might work there; either way, he's there right now.
Church:
He is in church. - Services are in progress right now, and he's there.
He is at church. - Interchangeable with "in church".
He is in the church. - He's inside the building; no information is conveyed about what he's doing there (he might be polishing the floor, for example.)
He is at the church. - He's on the church grounds, not necessarily inside the sanctuary.
University/ College:
He is in university. - Americans don't usually say "in university"; "in college", however, means that he's a student.
He is enrolled in university. - He's a student.
He is at university. - He's a student. This is much more common than "in university", for some reason.
He is in the university. - Again, we don't say this.
He is at the university. - The university is a local landmark and he's there now. (Who is he - student, professor, tourist? Not enough information.)
Prison:
He is in prison. - He's a prisoner.
He is at prison. - We don't say this.
He is in the prison. - He's inside the building. He might be a prisoner, a warden, a visitor...
He is at the prison. - He's on the grounds, not necessarily inside the building - he might be waiting in the car while his wife visits her brother.
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.
Best Answer
Normally questions with "Did you ...?" refer to a definite time in the past indicated with adverbs or adverbials such as yesterday, lately, last week, last year etc.
And normally questions with "Have you + past participle" ask about a fact with no regard as to when it was. A professor of literature might ask a student "Have you read Hamlet/Beowulf? The professor wants to know whether the answer is yes or no.
These are the normal uses, but in real life questions asking for facts are also done with "Did you...?" as has already been said in the posts above. Why? Well, I think in colloquial language it's a bit cumbersome to analye such questions and in fast talk there is often no time for such analyzing. So the grammar system is often simplified and speakers use "Did you...?" when actually "Have you ...?" should be used.