I don't use the Brother software with my MFC at all. My solution is to set up an FTP drop box on my desktop, and use the scan-to-ftp function. My MFC-9970-CDW kindly drops a nice PDF(several sub-types available)/JPEG/XPS file into the FTP drop box and I work with it from there. I haven't tried it, but it claims to have the ability to scan to Windows file shares as well, which would probably be easier to set up for Windows users. My wife doesn't even bother with scanning to her PC - she just plugs in a USB disk to the front port and has it scan to that. No big deal in her mind, since she has to walk up to it to put the paper on the scanner anyway.
For printing, of course, I just extract the PPD from the Brother driver package and feed it to Cups. Works like a charm, all printer features available.
Faxing might possibly be a reason to use the client tools, if you care about that. I haven't had an old-style land line in so long that I never had a chance to find out if the feature even works.