I guess, the most relevant would be logical variables to mark free trade agreements, double taxation treaties, then - similarity (or gap) in Doing Business indicators (say, time spent for property registration, tax reporting etc). I don't mean trade between countries value to GDP is not good indicator too (especially if the ratios are pretty stable). 

You may want to take a network perspective and see how the actors are all connected through various relationships (both formal and emergent) and flows.  Here is a simple network representation of the feud between UA and RU of natural gas flows to the EU.

http://www.thenetworkthinkers.com/2009/01/power-in-economic-networks.html

The methodology used here is social network analysis.

I second what Dr. Krebs wrote.  Additionally, the direction of flows and volume tells you who is dependent upon whom.  The areas useful for this analysis are, of course, economic, linguistic, currency flow, cross-border ethnic-based activities (markets, trade, etc.), correlations between voting patterns in international bodies (the UN), number of agreements, mutual participation in treaties, mutual participation in multinational military coaltions, where the youth go to college, where laborers go to work (cross-border?), where to do products and commodities go when bought or sold in markets where both states or corporations from both states are present.