I'm no expert, but I'm guessing that the rule of thumb is to use similar moods and tenses in each part of the sentence.

If we rearrange these sentences with the the "If-statements" first, it might be easier to analyze them:

1.) If she were alive today, she would have wanted you to become a doctor.

2.) If she were alive today, she would want you to become a doctor.

Both of these rearranged sentences start by using the past subjunctive (simple-past tense): "If she were alive today...." I would expect a similar use of the past subjunctive in the second half of the sentence to match the first part. The second sentence seems to do just that: "If she [were alive] today, she [would want] you to become a doctor."

Brian Garner's "The Chicago Guide to Grammar, Usage, and Punctuation" says that the past subjunctive really refers to the present or future even though it uses the past tense. This seems to fit #2 because it seems to be making a statement about the present.

If the first part of the sentence were making a statement about the past, you would have used the past-perfect subjunctive: "If she had been alive in the 1900s, she would have wanted you to become a doctor." Because the first part of the sentence uses the past-perfect subjunctive (had been alive), the second has a matching past-perfect subjunctive (would have wanted).

What do others think?