The fighting really, really sucks, but the story, characters and overall setting are reason enough for me to continue. It's something unique visually, at least. I suggest just playing through Infection, and if you like it, pick up the other 3 in that series (Mutation, Outbreak and Quarantine).
From what I played of the second series (.hack//G.U), I like that more gameplay wise. It's a much more modern game. Plus you can see the beginnings of CC2's ridiculously good animations and celshading in that (which really blossomed in their Naruto games on PS3)
For more opinions, check out Lindsay's great Anniversary Thread on the whole series:
http://www.neogaf.com/forum/showthread.php?t=468802