First thing I would say, is that the term "Alliance" is probably a hold over from Eve and the terminology makes us focus on the combat benefits of corporate cooperation only. While providing military support is certainly one of the reasons corporations would choose to work together, it's not the only one; Production is the other side of the Perptuum coin.
The game clearly promotes players to specialize to be most effective, and this would be equally true for corporations too, but there is no easy way for Corporations to cooperate. Recently PIE worked with another corp to produce some high-end goods that would have been a challenge for either corporation to do ourselves. Both of us being small corporations, literally in different parts of the world, weekends were the only time we were able to conduct business.
What I would invision would be a Logistics supply chain feature; we call it Extra-net here in the business world with tie-ins to programs like SAP. I'm not suggesting we implement SAP in the game, because that's overkill, but being able to place and fill orders between corporations would greatly encourage team play. This feature is something that smaller corps would find more usefull, hence promoting smaller corps, but not hindering the creation of larger corps.
As we see in the real world, even large compaines will subcontract out to smaller ones, the Build vs. Buy model. Or they may choose to aquire the company and run it as a wholly owned subsidiary; and this is where I think we replace the term "Alliance" with "Mega-Corp", simply meaning more than one corp. This is another level above 'extra-net' compaines involving a greater degree of integration between the corporations. The subsidiary's have a certain amount of autonomy but have to meet certain expectations from the parent corporation - be it production or number of combat troops.
Any cooperation feature has to mention outposts, and Mega-corps would technically share outposts, since the outpost would be owned by the mega-corp.