I think the NFL HOF has done a good job of keeping the standard of "can you tell the history of the NFL without this player?", for the most part, and it's a good standard. There are a few guys who I think meet that standard that aren't in (Coryell, Boselli, Bruce, Novacek, Nate Newton), but generally speaking that's the standard, it's a good standard, and they've stayed true to it.
Given that standard, it's really hard to argue against Eli making it. You can't tell the story of the Patriots without the kryptonite to their superman and without talking about the improbable way that the Giants made the Super Bowl as the 5 seed and took down the 18-0 Patriots (then did it again a couple years later).
He also has two Super Bowl MVPs. Here is the list of multiple-time Super Bowl MVP Winners: Brady, Bradshaw, Montana, Starr, Eli. I mean, it's definitely kind of an "lol one of these things is not like the others", but still, can't argue with results.
It annoys me that Eli will make it because there are probably 10 better QBs from this generation in terms of pure NFL QB ability. But it's not the "hall of being an effective player", it's the hall of fame.