First off I'd like to welcome you to the forums Sparrow94.
There are quite a few good points in your post that we have actually already thought of, but suggestions are what help make our title all the better for you gamers. I'll just take a moment to touch base on a few of the points you made. Please note that I am NOT a member of the game's design team, and points I make are not set in stone, though neither are the game designers really, as everything is pretty much up in the air until formal testing creates the foundation on which the gameplay will be placed.
Great Effects - We have plans to include ragdoll into the engine, however we are waiting to see if it is still technically possible, considering the amount of units we wish to have onscreen at once, of course a huge boulder that comes down would look great with a bunch of units flying from the impact, but as Darvin pointed out, we have to weigh eye-candy versus optimization.
Hostile Wild Animals - Also known as creeps as Darwin also pointed out, is partially one of the features we wished to have when we first started developing Dawn of Fantasy. For those of you who haven't been around since the beginning, the main premise of Dawn of Fantasy, is that we would supply an editor that you would be able to create scenarios from any fantasy base. Thus we wanted to include LOTS of animals, and creatures that both our designers and players could use to their own effect. Although I'm sure any aggressive creeps will be placed there by our map designers intentionally, we may also include an option to include them in multiplayer.
AI - I don't know if Darwin was mistaken, or if I'm looking at this the wrong way. As far as AI, you most likely will be able to fight an AI opponent co-operatively or on your own in mulitplayer. However I don't believe we will have an option to replace your own person with an AI during the game, we may have a feature where if a player leaves they are replaced with an AI concurrent to their ranked skill level.
Heroes - All units in DoF do gain experience not just heros, so there is a possibility that your units may come more experienced than them in the event your playstyle doesn't include heroes as a main unit. As far as custom-made heros go, it may be a possibility, it's up in the air if we will have sort of an avatar created to represent your MMO army.
Walls - Units on the wall will be targetable, and not be a part of the actual wall HP, if thats your concern. As far as near-by units being affected by the descrution of walls. I think this is a very good idea, as realistically there should be some splash damage done to nearby units. This would also bring a big twist to gameplay as it should affect friendly and enemy units, making siege ladders and other means of climbing the walls a more effective way to get around such defenses.
Make an Alliance While in Play - This will of course be included in MMO play as there isn't a point where you would join one before you start your MMO experience. Similarly, this shouldn't be a problem during a skirmish gametype, though the idea of using a messenger unit instead of a menu screen is a good idea.
Mini Hero Battelions - (First when I read this I misread the word Battelions, and thought, Battle Lions, thats an awesome idea!) But your idea is also a good one, one I don't believe anyone on our team has thought of. Though each unit is really unique to it's race, for example: Humans, Orcs and Elves all have a basic infantry unit, however each is different in play style and thus different. The races are not just the same with a different model to represent them, all the races are geared towards different play styles.
No Command Points - I'm unsure of this term, as I am not a typical RTS gamer. I would assume your talking about Unit Caps, such as only X number of units allowed. This will be determined closer to release, where we have an idea of how many units can be placed on screen with all the features and graphics we want.
Unit Upgrades - All units will have tech upgrades just like every other RTS, as far as will they save your units in a time of need? I'm not sure how the designers will play that one out.
Customer Made Banner - This was an idea I myself had suggested. This is probably the way we will distinguish players in the MMO portion of the game, although details are still being worked out. We perhaps will come up with a series of templates you can use much like capes in Guild Wars, to limit the amount of inappropriate designs certain players may use.
Ladders & Siege Towers - This will have to be up to designers and final testing, though as siege is going to be a large part of this game, it should be very balanced before it hits the shelves.
Hope I answered some questions, and alleviated some concerns.