1. It's API-driven, so we can modify our DNS entries programmatically. You can't do that with DNS Made Easy. (They've been "planning to implement an API in the future" for a long time now.)
2. At our scale, it's exactly 1/4th the cost of DNS Made Easy. That'll be a nice chunk of change. Plus, like other AWS services, you only pay for the number of queries that you actually use.
The reason I do this is so I can have the root of a zone pointed at an ELB, since you can't use a CNAME for that. So I mirror the IP address(es) of the ELB into the zone root. With DME, I rotate the IP every few minutes, but with Route 53 I could publish all its IPs. (Of course, it would be nice if Route 53 was integrated with Amazon's other services so I didn't have to do this at all…)
Has anyone tried this out though? My impression is that R53 is exclusively API driven, at least for now. I'd kinda like to have a web interface to fall back on.
They do provide scripts that take care of most of the work but ther is still more involved than a web front end.
For example you make changes in batches of records, and they can be create or delete. So to change an IP in an A record you make an XML document with both a delete request and a create request with the new value then poll the API for a sat us of in-sync.
EDIT: I forgot to ask, what kind of overages are you seeing? With Route 53 you'll be charged $501/month if your zone gets 1B queries.