Dear RG -
you will have only 3 full days in Galapagos. By the time you arrive and settle into your hotel, you'll likely only have a few hours of daylight left on day 1. On the day you leave on day 5, you'll have no time for anything except getting yourself to the airport.
Taking an inter-island ferry will eat up a good 50% of daylight hours, between the time you get out of bed and make it all across to another island and finish checking into your accommodations there.
So, if you do even one inter-island trip (read about the unpleasantness of such trips most of the time), you'll have 2.5 days on your hands during which you can organize visits. Going to Isabela Island requires at least two inter-island trips and more if you are including San Cristobal in your itinerary.
Under these circumstances, i would suggest you fly in and out of San Cristobal airport (5 minutes from town) and spend your entire time there. Organize your day trips (Española, 360 tour etc..) to interesting visitor sites now, and not on site. Otherwise, you'll lose at least another half day or more just trying to figure out what you want to do and checking to see if things are available or not. You don’t want to discover on site that things are booked up.
I lived in Galapagos for 4 years and have been helping people arrange their trips there for 22 years. You’ll have PLENTY of things to do out of San Cristobal for 3.5 days, trust me.
Warmest regards,
Heather Blenkiron