I used something like this to model a "Spirit Warrior" concept (if you know League of Legends, it was kind of like Udyr). The concept was a Native American Shaman who channeled different animal spirits to boost their powers. It was an 8 refresh game and I spent 7 on Modular abilities. The way I handled it was by stating out several sets of powers, corresponding to each spirit, before hand.
I think I had
Bear: Inhuman Strength, Toughness, and Claws. Basic tanky combat form.
Spider: Incite Effect (web) at Range, Venomus Claws (without the Claws, so only -2), Spider Walk. Secondary combat form, great for support via Web maneuvers/blocks.
Raven: Wings (these were concepted as shimmering spirit raven wings, not actuallygrowing wings), Inhuman Speed, The Sight (this may have been 3 eyed raven Game of Thrones influenced), Cloak of Shadows. This was likely the best form as it was perfect for scouting everything.
Coyote: World Walker, Demesne, a 2 cost home-brew power we had related to dreaming (in the Wheel of Time sense, this includes predictions and talking to people in their dreams). This was a cross between the concept of a spirit guide/spirit animal (which we chose Coyote for because of a Simpson's episode), and the Wheel of Time dreamer/dream world, where you shape things with your mind and damage becomes real. I don't think it saw much use.
We ruled that changing around the configuration was at least one full action (with no supplemental action allowed).
This character was fairly strong, as it was capable in combat as a support or as a tanky brawler, and had several other strong non-combat uses. I dont think it was too strong as it only had 5 refresh to spend on any one roll, with only 1 refresh level for fate points. It was weaker at any one thing compared to a character really specced out for it. Also, it has a sort of multi skill dependence since you need good fists (which was what incite effect was linked to, as a natural "weapon" of the spider) for spider and bear, good athletics/discipline/lore for raven, good discipline for coyote, and good might/endurance to make the best use of the other bear benefits. Since these did not come with beast change/true shape-shifting, it meant some forms were less optimal than others.
I hope that helps/maybe give you some ideas. I would certainly require that any character with modular abilities pre-define what sets of powers he can take and judge before the game if they are kosher. That is not to say that if he comes up with a great idea in game you should not allow it after the fact, but it will at least give you the option to disallow it if you feel it is necessary for any reason.