Question: If these were the best of the best, going on a mission crucial to world peace, why were they in aircraft that were outdated and outgunned? It mentioned several times they would never stand a chance against the dreaded "5th generation" enemy fighters. Why not use the F-35?
Answer: The real-world answer is that F-35s only come in single-seat configuration, so there was no way to put the actors in one seat for filming while pilots flew the plane. It would also make for less of an "underdog" feel of going up against overwhelming odds. The in-universe answer is that F-18s are better suited for the kind of mission it is.
Answer: Just my observation, but I got the sense that the F-35 was too fast to make the adjustment to do the steep climb out, and as much as the plane needed to be fast, but it was more important it be capable to throttle lower enough to maneuver through the course, and make the climb...and that the F-35 could do one or the other...just my guess, but that's how I understood it from Maverick's initial analysis, from when he was called in to "Teach".
Question: During training, Maverick says "The faster you navigate this canyon, the harder it will be to stay under the radar of these enemy SAMs." This doesn't make sense, shouldn't it be the other way around? (00:49:42)
Answer: I see your point, but he likely means that higher speeds mean they're more likely to gain height accidentally and be seen on radar. Basically flying faster makes precision harder.
Question: How were the ones who crashed/ejected rescued if they were in dangerous enemy territory?
Answer: You're correct - when you see Hangman's loadout before he lands back on the deck - he still has all weapons on the rails - it should be that he is short an AIM-9 or an AIM-120 AMRAAM depending on what was fired.
In all shots of Hangman's F/A-18E after the final battle (especially in the close-up right before he lands on the carrier), it is shown that there is an AIM-120 loaded onto the right air intake weapon station. The left air intake station is empty - indicating either no weapon was loaded or an AIM-7/AIM-120 was fired.
You can see that all his missiles are still intact and even if one is missing it would be very unlike to only load on the right and not the left as well. But where he says "This is your savior speaking" you can see all missiles are still on the plane and unfired.