Eli is far better than Tim Tebow. Did Tebow have 5k yards? No. It takes more than comebacks to be considered elite. Eli has comebacks+Superbowl MVPs+Superbowl Comebacks+5k yards. He also carried his team to the playoffs despite 29th ranked defense and 32nd ranked running game.
Also, Kurt Warner's idea of a HOF QB is different for everyone else's. Manning is a playoff monster. He just steps up his game in the playoffs plain and simple. He also has one of the best QB ratings in the 4th quarter, broke the 4th quarter touchdown record, and had six 4th quarter comebacks this season. That alone qualifies him to be in the hall of fame. You take one of those comebacks away and the Giants wouldn't even be in the playoffs.
Let's take every element you named here.
Eli has comebacks, that's great. He is clutch, but as I've told you ad nauseum, he is in the position to have more comebacks because he doesn't do a great job of giving his team the lead in the first 3 quarters. This is the exact same problem Tebow had that everyone criticized!!!
Super Bowl MVPs are typically given to the QB. When it is a team game and it takes an entire effort and no one player stands out, it is almost always given to the QB. Hell, you'd have to play pretty bad as a QB or have someone do amazing to not win the MVP. Nothing surprising about that.
5000 yards? Yes, he threw for a lot of yards this year. He had more pass attempt this season than any other point in his career. The entire league had more passing yards this year too though. I am not meaning to make light of 5000 yards, it is a great accomplishment, but it is not the same accomplishment it was 10 years ago. I bet we see another 5k guy next year, maybe a few.
None of this matters though, as the entire point of the conversation is that over his career, he has not consistently done these things. If he starts to do them consistently going forward, we can talk. But until then, this was simply a case of a good team getting really hot and having the lucky breaks during the playoffs. Nothing more.