I have no objections about seeing something that existed previously (whether from XI or not) being added into this game, as long as the reason(s) behind are legitimate and interesting. If it was put in simply because they ran out of ideas, then sure, it's a bad thing and has no purpose at all.

If, on the other hand, it serves a purpose, creates some lore and fits into the events, then what is the problem really. It seems to me that people are simply associating Atomos' appearance, not with the actual entity, but rather what it led to in XI. But even then, it's being associated with Abyssea over it's initial WotG purpose (it's relevant to both and fits well anyway). People need to stop bring those "OMG the game is gonna fail now that Atomos here" thoughts and just see how it goes. This isn't FFXI.

With regards to using previous concepts and such, there's probably going to be a lot of other things introduced into 2.0 that we've seen before (like Behemoths and that concept art of Ultima Weapon we saw that was ripped straight out of FFVIII and made a little prettier). It creates an air of familiarity and nostalgia and it makes me happy to see that inspiration (when new or old) is being drawn from older games. I'd get used to it, or don't stick around for 2.0.