Based on the original House Marik Sourcebook, the FWL is technically a representative Parliament style government. Notwithstanding the relative political power of the various Captain-Generals, each province (of which there were 154 in 3025) is awarded representatives in accordance with their tax contributions to the League (minimum of 1). There are a total of 500 representatives in 3025. The various larger provinces (e.g., Marik Commonwealth) are financially well-off and have lots of representatives; plus they can control their bloc of voting rights similar to political parties nowadays.
Minor provinces, most which are single planets or systems, still have voting rights, but not a lot of political clout, and they collectively make up something like 180 of the 500 votes in 3025. They are not under direct federal rule though (except see below).
There is also something called Resolution 288 that Parliament passed in 2779 giving the Captain-General essentially "emergency war powers" to control various parts of the League government, although not total control. That Resolution is still in place in 3025 and is the basis of the CG's power in the League. It is likely that Resolution 288 means that Minor Provinces have very little say in what happens to them. Since the Resolution lets the CG control the military (and the Mariks directly control/support a large chunk of that military with the Marik Militia regiments), the CG can park a FWLM unit on any world it wants to squash politically, whereas the larger Provinces would have more political leverage to fight back.