Myself and a few coworkers were talking about this today. It could be a good thing, if handled properly.
Cisco just needs to let Linksys run their own business, to help keep the prices down.
With Linksys they can get into the home and SOHO market where they couldn't before. Why buy a Cisco router for $1000+ when you can buy a Linksys router for $200?
If Cisco starts micromanaging Linksys then Linksys' prices will very likely start going up to cover the overhead (i.e. paperwork) that a company the size and power of Cisco could create...
Believe me, having a larger company micromanage a small acquisition is a bad thing. My company is going through this now... Budgets and pile after pile of paperwork and tracking everything, the politics... Not good. It's like information overload.
Cheers,
Sean