I'm curious why there is a problem with making "the file look messy?" Your users will likely never look at it (unless you are building something for JS developers) and the compression should really only be a step in your deploy (save, compress, run tests, deploy to server). So theoretically no one should ever look at the compressed files. That being said if you have a lot of JS it can really improve load times of sites but thats about it.

As for the 2 options you listed, there are 2 benefits of option 1 over 2 (given that no one is ever going to look at the compressed files). First, some JS compressors do a better job when they have all the files together as one large file. Second, consolidating them all down to 1 file significantly decreases the number of requests the client has to make to your server. This reason alone will probably have a bigger impact on your sites performance than compressing the files alone so I would definitely recommend you look into it.