I personally think the new changes to the company and alliance limit is a welcome and much needed change. The only downside is that the 4 company limit to alliance will force smaller companies to merge. I think that a significant portion of the playerbase don't want to merge into a larger company, me included.
A possible solution could be to make the alliance limit work like the sails limit on ships. An alliance could only hold a certain 'company points'. A company is worth a certain amount of point based on the company size. The company size is fixed and can be increased by buying an 'upgrade certificate' at a freeport.
For instance: your company starts with an ten player slot 'certificate' and is worth 0.1 alliance points. If you want to recruit more players, you have to buy a bigger player slot certificate, which will increase the alliance points of your company. You can't buy a bigger certificate if the alliance you are in is already at her max company points.
This way you can allow more than 4 small companies to form an alliance and prevent mega alliances. What do you think?