Your number 1 priority when auditioning for a music program is to highlight your strongest skills as a player. The teachers at Berklee, and every other major music school, have seen it all before and are not looking to be impressed. They want to see that you have the skills necessary to succeed in the program, and they're going to be listening to your time feel, note-choice, tone, overall musicality, your maturity as a player, etc... You're much better off playing a relatively simple or easier song that you can nail versus trying to cram "Donna Lee" into your fingers if you've never played it. If "What's Going On" or "Sir Duke" shows your best qualities as the player you are now, play those - you'll have plenty of time while at school to build up your chops.
Best of luck!