"1. There's intelligent life on other planets."
Probably.
"2. They have spaceships with very advanced technology."
Possibly.
"3. They're here, assisting the planet, but people don't see them because of the very advanced technology."
I find that incredibly unlikely. Why the hell would they care?
"It seems the 3rd part is where people have problems, but if you can agree with the first two it's not very far of a leap."
From one side of the Grand Canyon to the other is less of a leap.
"There's evidence to support it too, look up the Stephenville UFO case."
I'll be sure to do that. Or maybe I wont. I can't imagine what would make that any more compelling than any other such account.
"Or perhaps the objects seen by hundreds, some a mile long, were really F16s as the military says."
F16's? Uh, no. Military craft of some sort? Possibly. The SR-71 Blackbird was classified for 20 fucking years and people kept reporting UFO sightings every time it was flown. The military generally wont make any aircraft, or much of anything else, publicly known until it's way out of date (i.e. they've got a much better replacement).
There's also the possibility that it's simply mass hysteria of some sort. Orson Welles' War of the Worlds broadcast has shown how powerful that can be.
"They're up there, people see them all the time."
People see something all the time. That something just happens to be unidentified which, by it's very definition makes it a UFO. Something being a UFO does not make it an alien craft.