I would suggest go with WHMCS. You will get lots of option to manage various things related to billing as well as other things too. It is easy to install and manage. We use it from too many years without any hassle.
The automate billing reduces your time. It is very user friendly and secure way of billing.
Blesta and WHMCS are very good billing panels currently available in market. I have been using both for quite a while and have not faced any issues yet. I highly recommend these two billing softwares. Even WHMCS has not made a lot of updates recently.
Yes, WHMCS isn't that flexible and can't be customized to a greater extent. You can try using Hostbill and check if it fine for your needs.
I'm using Blesta Billing software and I can say it is great ,I just update few days ago to 3.2.1 version and it is great.
We really love WHMCS, I find it very good, but also like Clientexec which you may want to try it :)
WHMCS is the best billing software which includes a fantastic ticket system.
WHMCS is good, has a large number of addons and modules. Customizable as well
Clientexec we like has integrated helpdesk and does everything whmcs.
For me WHMCS is best one in that good features for client management
we use Clientexec and whmcs, all running smooth.