I've stayed in the park and outside of the park, and I'd definitely recommend that you stay on-property.
From your post, it sounds like you're driving to WDW. You don't have to use the Disney buses if you're concerned about the wait, you can still drive to the theme parks, water parks, etc. Parking is free for resort guests, so it won't cost you anything extra. And you still have the option of taking the bus if you don't feel like driving some days.
The WDW hotels are reliably clean and comfortable (I've never had a bad resort experience). You've got the food court right there; you'd probably have to drive to get a snack if you stay at the Comfort Inn. Big, beautiful themed pools. The theming really does make a difference...at a Disney resort, you're surrounded by all that Disney magic 24x7. At the Comfort Inn, you're in a plain old motel.
Unless money's really super-tight for you, it's worth the extra expense. If you're going to the expense and trouble to drive to Florida, buy passes, etc., you might as well spend a bit more and have the full Disney World experience.
Have a great trip!