I played in a multi-planar Savage Species campaign, based on the Nameless Legion scenario from Dungeon magazine. We found the book to be full of holes, unbalanced, frustrating, broken -- and terrific fun!
A few suggestions:
1. Make sure the players consider their race/monster choice very carefully from the get-go; the party's Werewolf-Pixie-Rogue didn't quite turn out the way the player wanted...take note of the SINGLE HIT DIE until 6th level as I recall...
2. Don't let anyone play a Ghaele or Astral Deva...Chain Lightning at level 6 just aint right...
3. Consider drastically limiting the stat-point buy of characters if you use that system; we used 32 (admittedly high-powered) - but this turned my Djinn into an insane killing machine (Str 22, Dex 20, Con 18, Int 18, Wis 14 or thereabouts) at around level 5 or 6. Add to this Invisibility AT WILL, Whirlwind (which simulates an 8th? level spell), perfect Flight, Large Size, Plane Shift AT WILL (hint: touch someone, shift to the elemental plane of Air, drop them, shift back - or, for that matter, the elemental demi-plane of ACID, to which Djinns have immunity), etc, etc - and you have a seriously broken character.
4. Consider limiting the stacking of templates. Another player made the most horrific thing I've ever seen constructed; a Feral Insectile Half-Ogre Psonic Warrior or something...only around ECL 6, and it had 20ft reach with a halberd and a climb speed - just picture it sitting on the cieling with a Large-sized Halberd...scary!
There are many more holes to look out for...but as I said - a tremendously fun game can be had with this book.
Good Luck!