The Arduino hardware abstraction layer has really been one of the biggest steps towards a more universal and interoperable set of software for bare silicon. Yet as you experienced, even then it wasn't enough to bridge the gap fully.
The fact that we call other boards "Arduino alternatives" is partially a testament to that. (Say, instead of "AVR alternatives")
It's certainly not perfect, always the fastest, doesn't expose all the features one might need, but it makes prototyping and portability oh so much easier. I'm glad we have something.
I'm sure there are good alternative to the Arudino out there. Arduino certainly wasn't the first to market with beginner friendly development boards and the popularity of Arudino only attracted more companies to the market. Unfortunately, it would be difficult to figure out who to go with since there is so much meaningless noise out there.