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We use simple past to state a hypothetical present situation that we would like to speculate about (If they were here, I would be happy), past perfect for a hypothetical past (had they been here, I would have been happy), and simple present to a hypothetical future. Any explanation why this makes sense, as opposed to past for past, present for present, and future for future?

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You seem to be confused both about terminology and tenses, so let's try to get this straight:

For present hypotheticals we use a form that is technically referred to as the subjunctive. The subjunctive is identical to the simple past in most forms, but you'll notice that it differs for the first-person singular:

If they were here, I would be happy. If I were rich, I would be happy. (Not: If I was rich.)

(Just to make things complicated, this form of the subjunctive is disappearing and many people do, in fact, say If I was rich. But for the purposes of illumination, let's treat this as a separate way of inflecting the verb.)

For past hypotheticals we use the past perfect (or pluperfect), not the "present past" that you referred to. (I've never heard the term "present past" before, and in any case I would interpret it as a reference to the present perfect, which is incorrect.) The reason for this is that the simple past is the same in almost all cases as the subjunctive, which is used for the present hypothetical.

If they had been there, I would have been happy. If I had stayed, I would have met her.

For future hypotheticals we use the simple present. This is not actually surprising, since the simple present is used for near-future events in a variety of contexts in English.

If they come, I'll be happy.

Note, however, that it's actually possible to use both the modal will and other future constructions such as going to in this construction, depending on context.

If they will reduce the price, I'll buy.

Here will retains some of its historical sense of willingness as opposed to indicating mere futurity.

If they are going to leave, then I am, too.

This is a pure future conditional. You can use going to for the future hypothetical in almost any case where you would otherwise use the simple present with no change in meaning.

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Thanks, Sorry I was meaning to say "past perfect" not "present past". And my question was asking about an explanation why they make sense, can you help with that? –  Louis Rhys Apr 4 '11 at 16:12
    
@Louis, I thought I had helped with that. To be clearer: the present conditional uses the subjunctive, which is similar to the past for historical reasons. The past conditional uses the past perfect in order to avoid similarity to the subjunctive. And the future conditional uses the present tense because the present tense is often used for future actions anyway. –  JSBձոգչ Apr 4 '11 at 16:27
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And the similarity of the subjunctive to the past is not because of any similarity of meaning, but because the particular grammatical forms in Old English (which was a more inflected language like German) have led to almost identical forms today. Compare German "er war" = "he was" (past) vs. "er wäre" = "he were" (present subjunctive). –  Colin Fine Apr 4 '11 at 16:59
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Note that we don't use just any subjunctive in hypothetical conditionals in modern English: were is the past subjunctive, as opposed to be, the present subjunctive (be they men or women, they shall die). Note also that if they had been is technically past perfect subjunctive, not ordinary past perfect. There is no difference in form, but that shouldn't be a reason to stop differentiating between these tenses; we also differentiate between be in he will be rich (infinitive) and in he requests that the goods be delivered (present subjunctive). –  Cerberus Apr 4 '11 at 22:39
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@Louis, Here is the Proto-Germanic verb: wiki.verbix.com/Languages/Proto-Germanic. As you can see, the subjunctive forms are not particularly close to the past forms, though subsequent sound changes made their distinctiveness less clear. The Proto-Indo-European subjunctive and optative are even more distinct. An example inflection is here: en.wikipedia.org/wiki/Proto-Indo-European_verb#.2Ab.CA.B0er- –  JSBձոգչ Apr 6 '11 at 13:11
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