CPU usage when the window has input focus is due to the blinking cursor. It's more of an issue when gpu_window_buffer is enabled, which it will be on any retina MBP. It has been improved in 3009, but more needs to be done: work is ongoing. As a workaround, you can change the caret_style setting to either blink, wide, or solid.
If you are seeing a reasonable amount of multiple processes, 16 or less per window, this is the expected behavior of the file indexing. There is a progress indicator in your status bar showing how this is going. You can disable file_indexing via the index_files setting, but this will also disable Goto Definition and Goto Symbol in Project. Some details are at https://forum.sublimetext.com/t/build-3009/8676/1. Please keep in mind that while CPU utilization will be high during indexing, all the indexer processes are running at a low CPU and IO priority, so will hopefully have a minimal impact on the system.
If you're seeing a runaway number of processes, more than 16 per window, I'd appreciate it if you sent an email to email@example.com