I am creating new web applications and creating a new app pool each time. Is there a downside to doing this?
Application Pools are fairly expensive. I will often advocate/build farms with the minimum number of accounts possible (for those covering App Pools, that would be a Farm Admin, Service App, and Web App account).
With .NET, there is minimal memory sharing between processes, and the SharePoint binaries consume quite a bit of memory without any end user activity.
The downside is: you can hit the recommended limit of 10 app pools: see https://technet.microsoft.com/en-us/library/cc262787.aspx#WebserverAppServer.
Also note the limit of Web applications (20).