I'll just echo what lacunae says, watch out for big strength builds. In the campaign that I DM, one guy played an ogre, pumped his strength, and was doing massive amounts of damage with his greataxe. Add in reach . . . ugh.
Unfortunately at that point in the campaign I couldn't just throw in some spell casters and exploit his low will save. He ended up getting a bit bored bashing everything and has since moved on to another character. To a human, incidentally.
Another player is playing a troll and enjoys grappling. Regeneration is tough to deal with sometimes; but since most folks know that fire/acid hurts trolls, it's reasonable for me to throw fire/acid damage the troll's way.
And I've also got a ghaele in my campaign. Yes, her special abilities are killing me sometimes, especially the incorporeal ball form with the color rays.
But these guys really struggled through the lower levels, to echo the point about low hit points. Now they're finally getting to the payoff, and they're enjoying it.
As a DM, you just need to make sure you take into account the powers when designing encounters. Now that the ghaele has hold monster, I make sure to throw in an extra monster or two (if they have low will saves). I make sure that any spell casters I create have a way out of a grapple, and when the ogre was in the group, I made sure that climactic encounters had at least one guy with lots of hit points.
Running a campaign with monsters is doable, just a bit more work for the DM when the monsters are fully grown.
