The idea of having an Apocalypse tournament occasionally gets suggested at G2D4. I usually cringe at the idea, as it comes in the form of a standard tournament with a high point value and super heavies. I immediately picture Aaron playing his bio-titan and killing everything while my super heavy fliers buzz around without a scratch on them. Apocalypse and Planet Strike were not written for a competitive environment, and if you told a GW designer you were going to use them as such, they would probably look at you like you just grew a second head.
Saying that, I think you could create a semi-competitive Apocalypse event with alot of careful planning and a good understanding of what Apocalypse is and what it is not.
First off, some logistical considerations:
Games with super heavies need space. At least 6x6 for 3000 points; 6x8 would be better. This would limit the event to 8-12 players unless a larger space than G2D4 could be found.
Time will also be a constraint. You'll be struggling to fit three 3000 point games into a single day. You are going to need to run it as a multi-day event, or impose some strong turn time limits. My thoughts are to impose 15 minute player turns, with 5 minutes to clean up any declared assaults. This would yield 5 turns every two hours. This would still require players to hustle on setup and between game activities.
Pre-submitted army lists(I'll talk about this more when I cover balance), and hard commitments from the players to attend is also a must. There's going to be a lot of planing required, no sense in doing it if every one is going to flake out.
Structure of the event:
I would split the players into order vs chaos and the tournament gets won as a team. The results of the games get pooled together to determine which side wins. The winning team should get some prize support, such as a dice cube or something in the 5-15 dollar range so that winning and loosing isn't such a big deal. This is important considering the balance issues. Give the best prizes based on a player vote for coolest themed army as this is basically a fluff event anyway.
I would run the tournament like a story campaign. Every scenario is selected for the specific player match ups. Wins and losses will take each player to another specific scenario against another player. Create a simple flow chart to assign the games. Don't enumerate every possibility as that grows exponentially vs tournament size. Do set up the flow chart so that there is no possibility of a player going into an auto loose game( i.e. the guy with no Anti-Air faces the guy with 3 fliers). Another reason why army lists need to be submitted before hand. Winners should still play winners if possible.
Don't score the games based solely on win/loose. Add story driven objectives that have more weight. Things like: Your HQ defends an objective against three turns of enemy assault(5pts). Make fulfilling fluffy based conditions the major objective for scoring points
I'd also have the results of certain games effect the tournament as a whole. Basically wins on certain tables grant assets to one side during the next game.
This is the most important consideration. Just like when GW wrote the Inquisitor rules and left out the points, GW wrote Apocalypse and left out the balance. The tournament organizer is going to have to add it in himself. Some hard and fast rules are going to have to get made, and somebody is not going to like them. Unfortunately there are some things that are going to need to be nerfed for the benefit of all.
Allow no player selected assets. Some are just broken, and can really throw off the game. Add them to any scenarios with careful consideration. This unfortunately means no formations that grant assets either.
Allow allying based on the allies matrix. This is a great opportunity to let Chaos Marine players use real demons. Every set of units from a single codex should follow the Force Org chart, but super-heavies and formations don't count against it.
Lists should be pre-approved. Screen out any lists that will steamroll every thing else. Don't let people take eight strength D templates.
Build the scenarios based on the lists. Be fun, use the army specific ones from Battle Missions where you can. If you have to match someone with no super heavies against a guard player with a line-breaker formation of Baneblades give him some emplaced defenses.
It ends up being more of a Campaign-In-A-Day than a tournament, but I think you could make a unique experience that captures some of the competitive environment of a tournament and the warm fluffy feelings of a campaign. It would take organization and a clear understanding of everyone involved that this is a FOR-FUN event, and to leave the A-Game at home.
You also end up breaking every rule of standard tournament organization. For any normal tournament I'm a firm supporter of playing the game as it is provided. No comp and no crazy scenarios or shenanigans. You pretty much have to take the opposite approach here, as the organizer cannot rely on the rules to make everything work.