Which one do you prefer? I prefer Rebuild, as I saw it first and Neon Genesis seemed to drag out a lot in the second half. Not to mention I was not to keen on End of Evangelion...
Guess I'll play the role of nitpicker from what I mentioned above.
Rebuild and the original series have some pretty significant flaws for me that hurt their quality for me. In Rebuild's case, the series is a bit more positive in its depiction of its characters (Shinji being less angsty, Asuka more likeable, Rei more human, etc...) yet it is lacking in depth to a great extent compared to the original series.
The problem with the original series for me is that the director (Anno) seems too intent in spinning his nihilist beliefs into the series where it gets difficult to relate to characters because they continue to be pathetic mental messes that don't grow out of their angst traps and the title's habit of slapping any kind of hopeful moment away to leave the characters as they are and build up to its infamous ending. The direction of the series also has its questionable moments that hurt its quality in later episodes (most notable, wasting the final two TV episodes for psych evaluations of the cast) and had some decent-sized plot holes with elements to its plot.
The reason I prefer the manga as the better adaptation of Eva is because it takes the better elements of both (TV anime's depth and Rebuild's more positive depictions) and combines them to create a more engaging story. Shinji still has his emotional baggage from Gendo's neglect, but is more relateable since he's become a bitter, angry youth thanks to his father. Rei's character has her growth as she comes to realize her growing humanity and establishes a bond with Shinji as the manga progresses. Asuka still has elements to her bitchy persona from the anime, but elements of her past are revealed early enough in the manga to reveal she has her own dilemmas as well. Essentially, the major characters come to get some sort of growth throughout the manga (unlike the TV anime) and while still having its harsh moments with depicting the TV anime's events (even having some alterations in events to shake things up), it is nowhere as nihilist as Anno's direction of the TV anime.