Agreed, whenever you make changes to the tried and true formula you have you have an AI who can understand the changes and take advantage of them. With any luck the AI's unit recognition is spot on with other parts of its development.
The AI has been coded for Empire with a lot of knowledge about how each unit type should be used(we also have a lot more unit types defined in the code instead of the old cavalry, infantry, spearmen, missiles) so it will know to use lancers differently compared to heavy cavalry for instance.

If a fleet was mixed between large and small ships, it was only due to limitations of logistics or economics. It wasn't an intentional mix for tactical purposes. That's just nuts. Every admiral would much rather have ships of the line in battle. It may not be as "fun" as mimicing land battles with flanking and skirmishing by smaller/faster ships, but the fact is that battles were won by big warships with the heaviest firepower (not to mention capacity for the largest complement of marines in case of boarding).
I think you're rather forgetting Nelsons famous quote on the matter of frigates:

"Was I to die at this moment, want of frigates would be found stamped on my heart"

Of course in a stand up fight they're no match for ships of the line, but there is a good reason to have frigates in your fleet in Empire, and it's for similar reasons for why they were wanted in real life.