MSBuild is great. It is similar in concept to NAnt, but slightly different with some of its tasks or implementations.
Once you get used to it, you will be cranking out the build files. Take a look at a csproj file, it is very similar to a MSBuild file (it uses a lot of the same structure but it technically isn't a MSBuild file). Building custom tasks for it is very simple, there are plenty of guides on teh interweb which walk you through how to do it.
If you are looking for alternatives, then i would go to NAnt. It is free, and has a huge amount of community support and extra tasks available. I haven't used it for a few years though, so i can't comment on its exact state at the moment.
There are no real drawbacks to using MSBuild, unless you count the amount of time it will take to get up to speed with it, and the amount of time you have to spend researching it.
From your questions it sounds like you don't really have much of a build process in place - take the time to do it, once you have you will wonder why you didn't do it sooner.