I suppose most of my negative experiences with it are specifically in the context of using it to build microservices. The memory usage alone created a bit of a problem, I ended up using nearly all of my 16GB of RAM when I had to run many services simultaneously. And because the functionality of any given service was fairly minimal, there really wasn't a need for a framework like that.
The autoconfiguratuon was also a bit dangerous. Since any dependency could cause any other dependency to reconfigure itself, it made it difficult to determine why things would break at times. At one point one of our libraries that used RabbitMQ behaved differently in some other services because another dependency saw RabbitMQ on the class path and started trying to use queues that didn't exist. Someone spent a day and a half figuring that out because the error was being swallowed by something else so the application was just failing to start with some crypic error. And when autoconfiguration wasn't enough, you'd sometimes find yourself needing to write dozens of lines of Java to do something as simple as connecting to a second database.
In general I found we tended to have less predictable or obvious behavior in our Spring apps, and they tended to be more likely to fail at runtime than I would've liked.
I usually get rid of @EnableAutoConfiguration and then selectively import the auto-configuration classes I actually want with @ImportAutoConfiguration.
A Spring developer once mentioned, on a mailing list post i have long since lost, that the autoconfiguration stuff is pretty much demo-ware. It's good for getting a simple app up and running fast, but for anything serious, you should import the configurations manually, exactly as you say. Fortunately, that's an easy enough transition to make at any point in a project's lifetime.
For me, I imagine the dropwizard guys sat round asking each other what the best servlet container is, web MVC tool, ORM, DI framework, etc, etc. and they choose the very best they can think of for a dev to work with.
Then a couple of years later that company comes along where they ask the same questions and but there's a guy with Tourette's in the corner and Every. Single. Time. the answer to the question is SPRING!! SPRING!! SPRING'S THE RIGHT ANSWER!! SPRING!
From the moment you boot spring boot and discover how much longer it takes to boot it's a struggle not to question the motivations of a place where the answer's the same no matter the question.
