not actually totally done with 6e yet but there seem to be only a few things that stand out as potential issues for the mega battle and a few more that could actually be helpful such as lists of special terrain type effects that could be stolen to add a bit of pre ruled flavor. one thing that could be a problem are the randomly generated warlord abilites, a few of them are compleatly unacceptable for a huge many person game. but that could be easily fixed if you just allow players to choose which ability there warlord has and make a short list of unusable ones.
but on another note the rumors are stating that codex legions will be out in the next month or two...possibly sometime in august, mabye it will be that august 4th date that was floating around for 6e for a while. If the codex lands even 1 day before the mega battle I would like the option of useing it for the mega battle this is how strongly I feel about how awful my Thousand Sons are at the moment, that one day of reading the new codex will still make for a stronger force than years of experiance with the current one.