It's pretty easy to script Keynote to export a presentation into PowerPoint format - just be aware that certain formatting/features may be lost due to functionality differences between the two, but you're already dealing with that.
This script will export the current Keynote presentation to the user's Desktop. Should be easy to expand that to save to any given location, as well as loop through numerous Keynote files - the main issue there is how you want to identify them: this script works on the current frontmost document, but it could be expanded to run as a droplet (drop Keynote files on the script to have them converted), or it could auto-run on a whole folder full of files, or it could prompt for individual presentations - you just need to specify what you want.
tell application "Keynote"
export document 1 as Microsoft PowerPoint to file ((path to desktop as text) & document 1's name & ".pptx" as text)
end tell