Planning a trip like that is work! If you get there and you don't have a plan, you will spend all day in line. Research the most popular rides, get there before the parks open, and you'll be okay. If you want to eat any table service meals at WDW, you need a reservation (ADR). And just to clarify, staying onsite at WDW allows you to make FP reservations ahead of time. They are now getting rid of what used to be FP machines everyone could use and instead using a kiosk system where people staying offsite can get FP the day of.
Honestly, if I were you, I'd wait a couple of years for Universal. They are building a new Harry Potter section at US that will connect to the Harry Potter section already in IOA, and it doesn't open until this summer. If you can only get there once, I'd wait until it's open.
There is no way you can stay offsite and do both Disney and Universal without a car. Rent a car. We got a car for $130 for 5 nights on our last trip. There are hotels that will shuttle you to Disney, but they run at limited times (often only every 30min). And they won't also take you to Universal. They are in two completely different locations, about 20 or so min apart.
Off the top of my head, these are the WDW attractions you need to hit first to avoid lines (and I cannot stress enough that you need to be there before the parks open. You cannot walk in at 10am and get onto these with short lines)...
MK- Space Mtn, Splash Mtn, Big Thunder Mtn
EP- Soarin, Test Track, Mission Space
Bummer that you are missing Expedition Everest at AK and Rock'n Roller Coaster at DHS, which are the two best Disney coasters.
We're also in the Indy area, and it was a good decision to fly.