This is largely going to be a matter of personal preference.
On a regulatory side, I have yet to see a fully 21 CFR 11 compliant software package from Agilent. The last I knew, Agilent was working on one (about 1 year ago), but this package was still largely a pipe dream. Empower is 21 CFR 11 compliant right out of the box.
Whilst, I agree that it's personal preference, needs also depend on your regulatory and work environment.
I doubt many labs can choose instruments solely on software functionality, they buy the hardware and local support, and then try to obtain the software that works best, usually consistent with what they already have to reduce training issues. Easy-to-use is very desirable for non-regulatory environments with diverse users ( eg walk-up instruments in research synthesis labs ) .
Software compliance to 21 CFR Part 11 is dependent on the installation and qualification, and I'm not great fan of Agilent's software, but the local support has been excellent.
I have no experience with Empower, but have used Chemstation for while. A local lab waited over 12 months for the local agents to completely qualify their new Waters HPLC systems to 21 CFR. The installer wasn't properly trained for the software, and the repair person wasn't formally trained to reinstall the software after an early repair performed under warranty.
Whilst working in a 21CFR part 11 environment, I found Agilent's Chemstore C/S system robust, if somewhat limited in integration and reporting. Cerity Standalone was/is a disaster, but EZChrom seems OK - so far.
As far as I know, Chemstore C/S and EZChrom are fully compliant when installed and qualified, as would be Cerity - until the first disappearance or lockup during routine operation.
Software is part of the package laboratories purchase to meet their needs, so users have to adapt, and every vendors package has strengths and weaknesses, so you work within those.
Bruce Hamilton