The multi pool I'm in (I believe it's the biggest currently) has been bouncing between LTC and DOGE a lot...  Both have a lot of holders (I believe?) and both have an already high hash rate.  I do not think the pool spends much time on small coins, if any.

I saw a few posts in "the other multipool's" thread where someone accused the pool of screwing up diff on a young coin.  However, the pool had only mined that coin once in 24 hours, only for a few minutes, and didn't find any blocks.

And, finally - multipool or not, there are two things that are fixed with altcoins (at least the scrypt ones I'm aware of)

1) The # of coins generated remains roughly the same regardless of hashpower.  The block time is the block time.  Multi pools don't make more coins, they just sell them faster than someone who is holding them.

2) When a multipool mines and sells coins, the coins don't cease to exist.  Yes, it may lower short-term demand, but whoever bought the coins on the exchange is going to do something with them.

If a coin is a strong one, I believe it will survive the multi pools.  If anything is damaging alts, it's the alts themselves.  Having set up a few coin daemons and compiled from source, I can say that it's hard to find any substantial differences between many of them.  Some don't even bother to change the name of the coin they are ripping off in the documentation.  The innovative ones will win.

Me?  I personally split the difference.  I have a little over half of my hashpower on a multipool (I have to pay for hardware and electricity after all), and the other half I'm bouncing between a few coins that I have faith in.  For those few coins, I'm in for the long run.