I am sorry, but I am of the opinion if you have presumably played the character all the way up from first level there is absolutely nothing "broken" about shapechange or any other 9th level spell. You have payed your dues, now reap the rewards.
Any "broken" aspects of this spell is supposed to be balanced by the fact you took so long to earn it.
Now, because a few DM's consider it too overwhelming it needs to be "balanced". I am the DM, it is as balanced as I need it to be.
As to the flea going into a mouth and becoming a Collossus, you cannot shapechange or polymorph into something when you are in an area that is not big enough for it. That is in the books somewhere. In 3.0 it may actually be in a splatbook or an errata. In 3.5 it is in the books. This is because you do not assume the shape, size, and powers of what you are turning into until you actually complete the change. If you can't get there you simply cannot do it. Nothing in the Shapechange spell says you can overcome limitations of space available.
As for all the other horrible abilities of shapechange. They are fighting CR 17+ opponents. If the DM is worthy of the title the PC's need every advantage they can get.
9th level spells should make your jaw drop. They aren't supposed to be "ho-hum" after "x" levels of adventuring to earn them.