The biggest effect would be if the flights in question are delayed. If American Airlines Flight 11 is delayed, then more people will be in the North Tower and thus more casualties. If United Airlines Flight 175 is delayed, then more people in the South Tower will survive and possibly the flight will be intercepted and shot down or otherwise miss its target, leaving the South Tower still standing, assuming the North Tower still collapses.
One other repercussion would be fewer recognizable and iconic photos and fewer photos as a whole. Might be fuel for conspiracy theorists.
No, there would be iconic photos, but there likely wouldn't be photos or video of the North Tower being hit, since there might not be a reason to call out the FDNY and the Naudet brothers, and they might not be able to capture their famous footage. But most of the famous 9/11 photos and videos are of the aftermath of American Airlines Flight 11 hitting the North Tower, and a lot of New Yorkers would turn their cameras to the smoking North Tower if the terrorists can still guide their plane to the North Tower. This adds to the conspiracy theories, but it's like the conspiracy that the Pentagon was never hit by an aircraft.
Assuming the conditions of heavy rain don't cause the terrorists hijacking United Airlines Flight 175 to collide with either Delta Airlines Flight 2315 or Midwest Express Flight 7, then they'll still succeed in their mission and hit the South Tower, which at that point will be watched by all the cameras and news media and result in the most iconic footage of the tragedy.
This particular talking point needs to die. Steel beams weren't melted and didn't need to be for the buildings to come down. What the jet fuel did is start massive office fires on multiple floors, and those fires consuming the ordinary contents of the building itself were sufficient to reduce the load carrying capacity of the already damaged structure to the point of collapse. The Lead Structural Engineer is on record as saying while they anticipated a 707 at low speed impact, what they had no way to realistically plan for was the effects of the fires after the crash.
Oh I agree, and so do most people who have actually done research. "Jet fuel can't melt steel beams" is/was a meme for a reason. Khalid Sheikh Mohammed (B.S. in mechanical engineering), Osama bin Laden (equivalent of a B.S. in civil engineering), and some other noteworthy terrorist leaders have degrees in engineering, and certainly they know what happens if you have intense fires burning in a skyscraper.