The rulebook in the Beyound Good and Evil expansion states that if you want to use the missions from Omega than the Area and Encounter cards are incompatible and should be removed. Having gone through the cards i cant see a reason why they cant be used. What have i missed, whats the reason why this is suggested?

I was thinking of using all the cards and choosing either the Omega or Good&Evil missions.

I don't see why the encounter cards should be incompatible, but the area cards are left out because if they're mixed in, about half of the area cards will have no relation to the Omega missions; any mission that requires that you go to a specific area (all of them, I think) will be harder to complete since you'll have to explore a lot more areas before finding the one you need, so luck will play an even greater role in completing your missions.

This is gotten around on most of the missions in Beyond Good and Evil by listing two similar locations (Summit of the Father or Fairy woods for instance), you could easily create a list of alternatives to balance this out somewhat if it was a problem for you.

However, one mission in Beyond Good and Evil lists only one Location (The mission to fight at Maisen), if this mission is considered balanced against the others if all areas are included I don't really see how the missions from the original game would be less balanced than before.

If you did use the missions from the base game as written the biggest problem would be a greater favouritism of the old locations, because only 1 mission out of 20 needs the new areas, but 10 out of 20 require the old areas. This could be solved by disallowing the new missions to utilise the old areas. (Making it 10/10 old/new).

If you didn't want that limitation because the luck is too great, you could take the time to develop alternatives from the new locations for the old missions (and then it would be more like 18 for both; with I think just the Maleketh and Maisen missions needing a set location).

I haven't tried this yet myself but I intend too after a few more games. (The game is fairly new to me), when I try it (utlising the new missions can't use old locations varraint first) I'll post how it worked out.

If you're worried about the final missons, to balance them is the same deal, you need to either limit the new missions to new only areas or modifiy the old missons to include a new area s well. Personally I think in the case of the final missons, you need to make the old missons more flexible to prevent (probably rare) issues in crisis mode where it's just impossible to get the mission started.

There's one more reason why you shouldn't use old missions with Beyond Good and Evil. Shadow of Omega didn't include Powerhouse named characters which are present in Beyond Good and Evil...hence the difficulty level of missions was fairly lower (and Shadow of Omega final missions were far too easy even without any Arcane character). If you really wish to mix all missions, you should decide new locations for old missions in new Areas AND rise a bit the difficulty of fights/check of old missions (a couple points should usually do the job). I know newer versions of Shadow of Omega have Crisis for Final Missions...unfortunately I bought the first edition, so one more problem for me would be to set Crisis time and conditions for the Final Missions from Shadow of Omega.