I've always disliked the "indexing" explanation. Partly, perhaps, because I've never seen a noticeable performance drop due to indexing following a major system upgrade. If indexing is taking a lot of resources and takes more than a couple hours, there's something wrong.
As to your particular issues, it's hard to say what's going wrong without more information. I was seeing a lot of beachballs and performance issues, especially when using Aperture or Photoshop Elements, until I upgraded my RAM to 8 GB (from 4 GB). You may benefit from that as well.
There are a number of other possibilities, as well as a test you can do to determine difinitively whether you need more RAM, in the second half of Understanding upgrade nightmares*.
* Disclaimer: links to my pages may give me compensation, and should not be taken as endorsement of my services by Apple.