Eli Manning is done and has been done for awhile. Eli has one winning season as Giants QB since 2012.
The rationale for drafting Saquon and keeping Eli at QB was that the Giants could win now as Eli is getting to the end of his career, and RBs have a short shelf-life. At 5-9, the Giants are going to have another losing season, and they still need a QB. So, if the argument is the Giants would be worse than the current 5-9 (btw, the same record as the Jets and Bills and worse than the Browns other teams with rookie QBs) with a rookie QB, that may be true, but you would now have your future QB to build around and closer to becoming relevant. The Giants are bad with a 37 year-old QB who will be worse next year. Saquon is a great talent. Fun to watch, but this is not a RBs league any more. Got to throw the ball to win.
FWIW, Eli is #22 in passing rating (behind Mayfield) and #30 in QBR, which also incorporates rushing ability (behind Mayfield and Allen, but ahead of Rosen and Darnold).
The argument in support of drafting Saquon is that the Giants felt that none of Darnold, Rosen, Allen or Lamar Jackson could be a long term answer. We shall see.