My guess is they will add options for additional indexes in the future...everyone needs start somewhere. Even at Amazon's size and scale.
At Amazon's size and scale, it's all the more important that you start with something simple with well-understood performance characteristics from day one. AWS doesn't really get a grace period during which they get to fix scalability problems.
AppEngine went the other route and provided a very simple database API at first and all queries had to be range scans over an index. Any query you wanted to perform had to be precalculated by defining a composite index and some things (like inequalities on multiple fields) weren't supported. Over time they've built upon their basic database and added features such as a zigzag merge join algorithm which lets you perform queries that were otherwise impossible with a given set of indexes.
I bet DynamoDB will be going the AppEngine route by starting with a simple, scalable base which can be used to build more advanced query engines and features.