Taqwus et al:
IMO, messing with the treaty system like that is a bad idea. That allows the players too much freedom to pick and choose the effects. I personally like having to weigh the good with the bad...you want the money, you gotta pay the cost in letting the 'alien influence' into your area.
Remember that the econ and research ponits provided are abstracted and represent ships and units 'too small to be tracked'. These guys are coming in and trading with your worlds...so of course the other government wants to send in 'police ships' and other vessels to 'safeguard their nationals' etc. Also, "while we're at it, we should expand and have a colony in there to help with our trade mission...after all YOU aren't using that world and shouldnt object to your good and dear friends moving in."
In all seriousness, I think the diplomacy could use a little work. But, IMO, removing all the 'baggage' that goes with the treaties is not only unbalancing in game terms, but unrealistic. You have to be willing to tolerate a certain amount of interference and influence if you want to have an ally/trading partner.
Talenn