If anything, transport ships opened the campaign map up more than ever. The AI still wastes it's armies doing nothing in the middle of nowhere, or wastes it to attrition or whatever, that's the nature of the beast. The AI of Rome 1 and 2 aren't very comparable though.
The campaign should be sandbox. Shogun 2's AI was the best at empire building and as a result i don't think it is any mistake that it is regarded by many as the best in the series. The AI does understand preservation, defending core provinces, recapturing lost territory, as much as an AI can understand it, there are even references in the database to terms of that nature. The problem is that with the introduction of the province system CA couldn't just build on what they did in Shogun 2 and they haven't done anything with it since. The CAI in Rome 2 and Attila cannot handle the province system, that's why you'll never reliably see empires built.
You are right that the CAI in Attila and Rome 2 is great for horde mode, but Shogun 2's wasn't.