I've looked in this direction as well. Some thoughts:
Geronimoo's simulator is ridiculously fast. Currently the code is fairly tightly coupled to the UI and card play rules, but I don't think it'd be too difficult to extract a jar that you could send XML files to and have it play the games with bots specified in those files.
Dominiate is much slower. Since bots are CoffeeScript programs, I think it'd be much easier to implement EC algorithms using the simulator, but it will spend a longer time crunching numbers.
Neither is all that great when it comes to tricky cards like Menagerie and Possession. For that reason, and for EC in general, it will be much easier to pick a well-defined problem. Something along the lines of optimizing Big Money + X, what sequence to buy victory cards vs money, etc.
For two similar bots, the margin of victory for one over the other can be pretty low. You may need thousands of games to be sure you're looking at signal and not noise in the win/loss percentages.
I've personally looked into implementing a pure Dominion API for this type of thing (also for bot competitions), but I'd want it to be something that both Dominiate and Geronimoo's simulator could use, and Geronimoo's is just too damn fast to replace.