I'm not exactly sure what you mean by "planetary alliances." Are you saying a group of allied planets, or an alliance of different sovereign government on a single planet?
One of the absolutes of membership eligibility is that the planet is united under one government (that obviously meets certain standards). So, while an alliance of a number of governments on a planet my be a step in the right direction, but the Federation would probably wait until the entire world is united.
If it's the former situation (an alliance of a number of planets), the Federation would probably consider the alliance as a whole. Of course, each planet would be investigated, to ensure that all alliance members are up to Federation membership standards. Now, if there are worlds within the alliance that do not meet the requirements (in some civil rights issue), the Federation may only extend membership to some worlds of the alliance, and not others.
Needless to say, a situation as complicated as that would be a hot topic of debate, and may call for a "Journey to Babel"-style Federation Council conference to decide the issue.
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz