It has a Spam box.. And your normal Mailbox..
You can sort out your main in archive or Later by dragging it left or right...
It helps you sort out mail with todo lists... You can set-up mail to sort of show up later so you can deal with it...
i.e. somebody might say your appointment is at 8pm tomorrow... And you want your mail to show up or remind you at 7pm the next day or in the morning of the same day...
Its sort of integrating to do lists...
Im am still using apple mail... I am happy with the whole notification/yosemite integration..
My todo list's are covered by Wunderlist and Evernote at the moment.. Evernote is an amazing program.. I can email a mail to Evernote specific email and catagorise it, and set up reminders etc... Evernote pretty much helps with everything i do.
But I am checking out Mailbox carefully for the future.. It seems promising... I like dropbox so i decided to give it a chance. Wont jump into it yet.. But playing with it.
Just thought I would let you know about it since you are actively looking for other options.
Since it is still a beta I wouldnt necessarily recomend switching right now...
But I thought it was a very well thought out approach to organise and act on mail from multiple accounts.
Just thought I would give you a heads up. It may be solid contender in your search for something that suits you. So far I like what I see..
There is a learning curve in using it correctly however. Its a bit different to your std. mail apps..