What we do with certainty is that as long as Pakistan is involved in America's war with Afghanistan, Pakistan cannot move forward with much needed economic development. Without the benefit of classified documents, I cannot state with certainty that Pakistan invited the US on its soil as a launching base against the war in Afghanistan. Pakistan has had a long-standing relationship with the US, from the Baghdad Pact (1955-1979), to a special military deal when the Soviets invaded Afghanistan, to supporting the Taliban that Iran and Russia opposed, to caving under pressure after 9/11 when the US decided to bring down the Taliban regime and hunt down al-Qaeda.
The evidence that does exist indicates that Pakistan had no choice other than inviting the US on its soil or facing bombing. Pakistan does receive at least $10 billion in total US aid in the past ten years, but the cost in political terms as well as economic is hardly worth the foreign aid; at least this is how many analysts see it from Pakistan's perspective rather than that of NATO allies. Without classified documents to tell us what goes on in secret negotiations, without intelligence reports to tell us what Pakistani intelligence has been doing in supporting or undercutting the Pakistan-US alliance, I must conclude that Pakistan as the weaker country under US-NATO military occupation, is at a distinct disadvantage at the very least, and a temporary semi-colony at worst. If a percentage of Pakistanis see the issue from this perspective, then we in the West must at least consider if not respect their view and not insist on a Euro-American-centric perspective to the exclusion of all other.
Furthermore, at present there is no prospect of an Iran-Pakistan nuclear axis, but even if there were down the road, it would still mean nothing more than diplomatic/geopolitical leverage that can easily be countered by India, Russia, China and of course Israel and the US, not to mention France and UK. Finally, given that Iran wants to be the major regional power, given that Pakistan-Iran relations were rather hostile in the last three decades, especially in the 1990s, Iran would only consider a Pakistani alliance as a last resort. This also because of its relationship with India that has been supportive of Iran's nuclear program.