Warning! Spoiler info to follow
Manga vs OAV
Angel Sanctuary's OAV is three episodes long, the manga is 20 volumes long. This is a very obvious difference, therefore let me assure you that the entire manga does not fit into these three episodes - only the first three graphic novels and part of the fourth are covered. Personally, I believe the manga is better than the OAV, but I don't think the OAV is bad by any stretch of the imagination. It skips, basically, from plot point to plot point, and cuts out any cute sections the manga had going straight to what counts. Certain characters were taken out and replaced with other people, or combined with another person. For example, instead of Ruri ever actually being in the OAV, they just have Rociel doing everything. The game "Angel Sanctuary" is taken out of the OAV completely. It's a mystery as to where Rociel gets the strength to rise again. Instead of Kirie attempting to kill Setsuna, Katan is the one who commits the deed.
Some of the things that they did in the OAV differently from the manga annoyed me...instead of Setsuna breaking the ball that almost falls on him from that tower, Arakune destroys it while attacking him. Whereas the scene was pivotal in the manga, showing Setsuna that at some level he had powers he wasn't aware of, it had a different air about it in the OAV. Katan was supposed to be doing all he could to keep innocent people from being involved in what was going on, for example, in the manga he tried to stop Kirie from delivering the killing strike, but in the OAV he kills her himself. As this is a huge "No" for Katan's character, it is probably the change I hate the most. The OAV ends with an ending that makes you scream for more, but unfortunately that's all there is.