The rental companies are used to people coming on flights that have been delayed. As long as you get there before they close, it won't be a problem. But, if you are going to get there after your reservation time, just give them a call to tell them your flight was delayed, and it won't be a problem. So, long story short, give them your best guess when you'll be there (if you get there earlier than the time on your resevation, the car may not be ready).
We rented from Dollar at the Regal Sun last December. It's literally across the street from the bus stop at DTD, so that will work fine.
I never took the DTD bus from POP, so I don't know how long that will take, or how frequently the DTD busses come, but I imagine that it can't possibly take more than an hour. So, if you are at the POP bus stop by 3:30, you will make it easy. Leaving a full 90 min (just in case) from gate to resort, a flight arrival time before 2 should give you plenty of time.
PS if you're running late, you can check in at POP after you get the car. Just go right from the ME bus to the DTD bus stop.