I noticed similar behaviour that QVP connection seems to be working slower in terms of report generation time, however it is more stable connection in terms of resource management and server stability.
My example is a small report which usually takes about 3-4 min to run on LOCAL connection, but it takes 10-20 min to run on QVP.
I know Qlik is working on speed improvement, but i am not sure how far did they go. Obviously a lot depends on your connectivity between NP server and QV server and how busy QV server is.
Do you struggle with resources on QV server?
How big is a report and how big is an app used as a source for connection?
Is it dedicated app meeting all restrictions? (no always one selected value, no triggers, no alternate states...?)