"I want to ask you."
Translation:Θέλω να σε ρωτήσω.
The structure is dictated by the verb used in every case. Some verbs are followed by their object straight away while others take a preposition before an object. Personal pronouns in Greek have strong and weak forms, with the weak form preceding the verb. Notice how the weak form is in a different case depending on the full sentence structure dictated by the verb in the following examples.
1a. Δίνω το δώρο - I give the present. (verb+direct object)
1b. Δίνω το δώρο σε αυτόν. I give the present to him. (full structure, preposition needed, the pronoun is the 2nd, indirect object)
1c. Του δίνω το δώρο. - I give him the present. (Indirect object in genitive case)
Same as above 2a. Λέω κάτι. - I say something.
2b. Λέω κάτι σε εσένα. - I say something to you.
2c. Σου λέω κάτι. - I tell you something.
3a. Ρωτάω κάτι. - I ask something.
3b. Ρωτάω κάτι τον Πέτρο / αυτόν. - I ask Peter something. (there is no preposition here therefore the direct object is the one referring to a person.)
3c. Τον ρωτάω κάτι. - I ask him something. (Direct object before verb in the accusative)
4a. Η καθηγήτρια διδάσκει λογοτεχνία. - The professor teaches literature.
Η καθηγήτρια διδάσκει τους μαθητές λογοτεχνία. - The professor teaches the students literature.
Η καθηγήτρια τους διδάσκει λογοτεχνία. The professor teaches them literature.
It's great that you've taken the time to give such a thorough answer, but I'm not sure that you have actually explained why the example question is using σε.
The answer to the question is ...σε ρωτήσω but in your example, 2c is σου λέω...
Neither have prepositions so I'm still confused when to use σε or σου.