I'm assuming this is planned to be a regular event on an annual/semiannual/something basis?
I don't know about the rest of you, but I don't see a whole lot of point to watching Stockfish and Komodo beat up on Crafty and Nirvana. There are a lot of games that are pretty one-sided. But those lower-rated engines are still inhuman monsters and can play some very competitive games against each other. I don't see any reason to shut them out entirely.
There are also a lot of mid-table battles that might make interesting games as standalone games, but aren't really relevant to the tournament as a whole, because there's no meaningful difference between finishing 11th or 12th.
It might be interesting to split the tournament in two and have an upper tier and a lower tier. 12 engines in each division. After the tournaments are complete, the top two in the lower division are promoted for next time round, while the bottom two in the top division get relegated.
To add new engines in later tournaments, you could either increase the size of the lower division, or relegate the bottom two engines and have a qualification tournament. Or, if you want to add a large number of engines, add a third division.
And you could still have a second and third playoff round following the current format (or something similar) to determine the overall winner.
This would accomplish several things:
1. Every game would be move competitive. We would no longer have the big three beating up on weaker engines.
2. The games that are currently meaningless mid-table battles would instead be part of a competitive promotion/relegation battle. This would create an extra incentive for engine developers to attempt to strengthen their engines a little bit to win promotion or avoid relegation.
3. Instead of a double round robin, you could have a quadruple round robin in each division, while having slightly fewer total games. Currently there are 23*24=552 games (you don't have to divide that by two because it's a double round robin). If there are 12 engines in each division, a quadruple round robin would have 11*12*2=264 games in each division, for a total of 528 games - 24 fewer than the current format. So in terms of CPU time, this would be slightly cheaper to run while having each engine play twice as many meaningful games against competitors closer to its own level.
There is one potential drawback. New engines that show up on the scene (like Leela) will have to work their way up through the lower division before they can compete against the top engines. But if these tournaments are run somewhat regularly, that's not a big deal. Most new engines that show up aren't top 10 engines when they're first released, so having to start in the lower division and win promotion isn't a bad thing.