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 Build 3009. 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 support@sublimetext.com