And you're telling me that some races in the book were so bad they didn't compare well to standard races from the PHB?
Yes and no.
Savage species allowed you to play powerful races with a high ECL from 1st lv by breaking it down into a class level format. For example, a fire giant (ECL19) could be broken down into a 19-lv progression table. At each lv, you get some features, and at lv19, you are effectively a fully-fledged fire giant. There was no such thing as a base LA+0 fire giant race, because you had to finish the progression before you could take your 1st class lv.
So in theory, a fire giant should be on par with a lv19 fighter using a core race (say either human or dwarf) in terms of how meaningfully it can contribute in a standard 4-PC party. Though in actual gameplay, it appeared to be much weaker.
However, this appears more an issue of the designers failing to assign appropriate LAs/ECLs to the monsters, rather than any inherent flaw in the concept of a savage species progression. It was rare that a monster PC broke the game. So if those inflated LAs could be revised, it would be possible to have a balanced PC that was still a blast to play.
The allure in using them was for the unique gaming experience of being able to access special abilities normally reserved for monster adversaries (and normally unavailable to PCs) and the chance of playing an unusual race/monster (and the accompanying roleplaying rammifications).
For an example, I refer you to this thread -
Such Tangled Webs They Weave: Assault upon the Abyssal Fortress [Archive] - Wizards Community, which involved a small group of celestials on a mission in the abyss.
It doesn't really have anything to do with the current discussion, that much I admit. I had simply made that statement I did earlier more as a passing remark about my incredulity as to just why so much emphasis had to be placed on the core races, and so little attention on more monstrous/exotic races. But then you tried to link the use of Savage Species to powergaming, and I felt that I just had to clarify this common misconception that monstrous PC = munchkinism.
The same scenario seems to be replaying itself in 4e. When you cite the MM provision and disallow a monstrous race as a result, are you doing it because you know for a fact that said race really is overpowered, or are you doing it simply because it is a monstrous race (and you assume that all such exotic races must surely be overpowered by default)?
Lets set aside the minotaur, since it has already been revised. The warforged for instance, was actually underpowered (since it received a boost in the dragon article).
Because if the race really is too strong, you would have a valid reason for not allowing it in your games, even without having to cite that clause. Conversely, if you use that clause as an excuse to disallow a particular race, than you really wouldn't care even if said race was perfectly balanced now, would you?