Can you have more than 3 banners in a deck if they are not the same kind of banner? For instance, can I have 3 High Elf/Dwarf banners and 3 Empire/Dwarf banners in the same deck? My first thought is yes but I did see some debate on the forums about this a while ago so I wanted to make sure.

You can have 3 of each individual card name. And must follow "order only" or "destruction only" depending on your deck.

Sweet, Thank you so much!

Right, there was some debate on this. The issue is that the title of the card is in a different place for supports vs. units and that caused the confusion. Yes, you can have 3x the different types in a deck (for a total of 9 alliance banners).

I think at the moment, I would consider the card number at the bottom of the card the ultimate identifier. I'm pretty sure even the new printings of innovation came with their core set number.

Technically, in the rules, the 3 of limit is specified by the card title. That's why this discussion came up originally - whether the title of the banners is "Alliance" or e.g. "Dwarf/Empire Alliance" (it's the latter).

Yeah, sorry that wasn't clear at all in my original answer. I didn't quite understand which question was being asked.