Thanks for your replies, Chris and Sounds. Incidentally, Chris, a significant factor in my electing to purchase this game was the community and the unprecedented communication between the company and its customers. Way to go.
I didn't have access to my iMac when I wrote earlier as I was out of town. I have not yet updated my iMac to Yosemite, so I thought it'd be a great test. I got back today, and I loaded up Last Federation right away. It worked flawlessly, lovely and smooth. I strongly suspect that the problem lies with Yosemite, especially because the pauses lock-up the entire system.
Sounds, the problem manifests for me on my Yosemite MacBook Pro within seconds of entering any tactical battle. It's entirely consistent from the get-go. Is your Mac updated to Yosemite as well? If it's not affecting all Macs with Yosemite, maybe it's limited to only some installations. My MBP has shown the WindowServer issue, and I think issues with Last Federation might actually be WindowServer malfunctioning. Have you encountered the Yosemite WindowServer issue?
In case you've not encountered it, this is an issue where the WindowServer process malfunctions and begins eating up resources and CPU cycles. It can slow the machine to a crawl. While I wasn't experiencing this at the time I was playing Last Federation, I think there could be a relationship nonetheless.
In any case, I will try Chris's suggestions next time I load the game up on my MBP. Hopefully Apple will release a fix within the next six years.