Could be anything, and without more information there's no way that anyone's going to be able to offer useful help.
To start with, what's the wait types the query gets? What's the query? What are the table definitions? What indexes do those table have? What does the execution plan look like? What's the CPU and duration? Are there still scalar functions (that don't count towards the logical reads displayed) and if so what are their definitions?
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)SQL In The Wild
: Discussions on DB performance with occasional diversions into recoverability
We walk in the dark places no others will enter
We stand on the bridge and no one may pass