One of the features we wanted to include in Clones was the concept of a "Boss Battle", where the player is essentially playing multiplayer vs. the computer. This turned out to be a huge problem and we had to settle for the current "Multiverse Match" CloneMaster battles in which a pre-recorded solution simulates head-to-head gameplay.
Creating functioning practical AI for this style of game might be impossible given today's hardware. Here is a paper that talks about a pathfinding algorithm for Lemmings: http://www.cs.nott.ac.uk/~gxk/papers/cec2004kts.pdf
The problem is even more complex in Clones because pathfinding is just one aspect of multiplayer, there would also have to be a sabotage algorithm and an active-defense algorithm all executing in real-time and computing successful strategies for situations being encountered for the first time. If there are any computer science students out there looking for a Ph. D. project to tackle then please let us know, a team effort would be welcomed