Sides and Countries

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As long as there is an ActLike=side that makes one sides settings all default to another sides I don't see a major problem aside from a question of need. Countries have traditionally been the most specifically customised organisational unit in RA2 so I'll dissent and say I don't really buy the argument for moving the customisation back up to side level. I'd say side should really be used to specify things like the UI, eva and the notion of a base build tree while country controls the specific stuff like stat bonuses like build speed or special units. Had the game used sides to do this from the start then I'd agree with what you are saying, but it doesn't make much sense to change it now to me unless there are technical reasons in terms of optimising memory usage or something.
For the example of paradrops, make it country specific with an owners list or a required and forbidden countries list as is already done for units. Modders can then make customised copies of a super weapon specific to a side or country as is their wont.