Maybe breaking this down in a "Tale of the Tape" format might make more sense since these guys are so close? I'll use the common factors I personally look at when breaking QB ties.
Track Record: Manning. I have a complete body of work from Eli and I know basically what to expect. Cassel has been a starter for exactly one season since his senior year of high school and is entering a completely new situation. Cassel may possess slightly higher upside, but only if KC aggressively improves his weapons.
O-Line: Manning. Giants have one of the best in the NFL, KC's was once elite but is currently rebuilding.
Running Game: Manning. Jacobs and Bradshaw vs. an aging Larry Johnson and dynamic but unproven Jamaal Charles. If I'm a DC and only have to worry about defending against a 3 yards-and-a-cloud-of-dust running game, I'm committing more assets to stopping Cassel.
Receiving Corps: Cassel. This judgement is solely based around Dwayne Bowe. He's an elite talent and legit #1 WR that the Giants don't currently have on their roster. Losing Gonzo will make his life infinitely tougher in 2009 though. I may give the Giants the nod on overall depth, depending on how their rookies and young players step up after losing Plax and Toomer. If they end up trading for Bolden or Braylon, this vote will obviously swing to Eli.
Divisional Strength: Manning. Surprised? Take a look at the defensive backfields of the AFC West vs. those in the NFC East. Obviously the overall quality of teams is no contest (NFC East), but Cassel won't be going directly against JaMarcus Russell or Kyle Orton twice each. He will, however be going against Antonio Cromartie, Champ Bailey, and Nnamdi Asomugha.
So, in my little world, Eli Manning would get the nod over Matt Cassel if I'm dead set on getting my QB1 in the middle rounds and those 2 are sitting there. I like safe, conservative picks over risky guys with upside if given the choice, and at least for this year, that leads me to Mr. Manning.