Just because it is harder, doesn't mean it shouldn't be done. As for it being harder, that is very much debatable.
The economic side of CN does need an overhaul though (IMO), even more so than we need more military features. Especially when it comes to resource trading. When I lose a trade (lately to deleted nations), it can take upwards of fortnight of sending out regular in-game messages, trying to find people who are willing to trade. Personally I'd love to see an in-game resources trading screen, where you'd be able to not only see what resources people have (in the current advanced trade search) but also what resources they are after. It would potentially cut down the time.
With tech though, I agree that a similar thing shouldn't be done, quite simply because its an in-game bypass of the increase in tech prices.
The stock market, economically, has nothing to do with alliances. It is a way of measuring the value between companies, not alliances. Leave it as it currently stands, a pretty wonder with nice bonuses.
Diplomatically, I'd say leave it on the forums. While implementing treaties between nations would be relatively simple, if you were to go one step further and try and implement treaties between in-game alliances, you run into problems. For one, how do you determine who has the permissions to add/remove/edit treaties? So as I said, diplomacy/politics should be left on the forums.