Ahh, so that explains why I couldn't have Honchkrow in my battling team. At least it's good to know that I can at least have my Honchkrow as my pet Pokemon.
As for the themes, the Don theme fits for my overworld theme, yes. And for the DK one? Definitely for the hideout. It has that industrial appeal that Team Ultima strives for, while giving it that dramatic edge.
Also, I do have an idea for how Team Ultima can reach its goal while causing more havoc. The machine Imperius is going to use is a huge weapon, right? Well, what if there were smaller machines to help reach that cause quicker, distracting the heroes while Team Ultima searches for Cresselia and Darkrai to power the Ultimate Machine? Remember how in Reborn there are PULSE machines, and in Rejuvenation, there are Dimensional Rifts? For the name Ultima, I like to think that the name means Ultimate Power or something like that. So, I'm thinking of calling these new machines the SUPREME machines. SUPREME would stand for Super Ultimate Pokemon Rehabilitation Engaging Mega Evolution. PULSE machines and Dimensional Rifts are like Mega Evolution, right? Well, SUPREME machines are pretty much self explanatory. They would create super ultimate Pokemon that are engaged in rehabilitation that causes a Mega Evolution that is similar to what PULSE and Dimensional Rifts do. For example, a SUPREME-Abomasnow could create devastating blizzards that could freeze an entire town, and a SUPREME-Malamar could brainwash an entire city! These could also probably contain Legendaries, too. For example, a SUPREME-Heatran could create a series of magma pools, or build a useful volcano hideout. Maybe more could be useful, but Heatran was the first I thought of.