Using Plunkett as a comparison to Eli is a bad one just because he won the same amount of SBs. Eli was not elite when he won his 1st SB during the regular season, but he was above average, then he was lights out in the playoffs, last year, Eli was one of the best QB during the regular season, and got even better in the playoffs.
Plunkett was a QB that never looked as good as Eli, but he did have elite talent (Reason why he was picked as high as he was by the Pats), including one of the tightest and best looking Spirals in the NFL (At that time, Tommy Kramer from the Vikings and Plunkett both had the best looking balls every game), which helped him put very catchable balls each game. If you remember Plunkett, you will also probably remember during the Raider and Flores years, he was thought of as one of the better QB playing at that time, yet at his best, never was he as good as Eli has been looking these past 4 years.
No Marcus Allen for Plunkett, the Raiders probably don't even reach another SB, yet take another good QB with Allen, they probably still reach and win another SB. As for Eli, there is no player in 2012 that wa not there in 2007 that would hurt the Gaints from again reaching the playoffs and winning another SB....unless that player was Eli, then the Giants would probably fail this past year.