The real problem is not that a new mail system was needed but they have once again implemented a feature onto the live servers incomplete with numerous issues raised in beta and duly ignored.I really disagree with a lot of the issues with the new message system.
Give it time to get used to it, the old message system was terrible. Threads disappeared at random, threads you sent didn't appear in your mailbox till they were replied too if at all, people were apparently deleting threads without reading them often meaning you were not communicating with them in the way you thought, it was only on PC, you had no idea what the last message you read was (okay you probably did but not as quickly as now).
While this has it's bugs as well, the mailbox only flashes occasionally (I think switching to GVG and back will reset it but that isn't good enough) overall it seems much more robust. I would like a slightly higher contrast or bolder font in mailbox (like the one that shows up when you are typing the message).
Guilds will get used to it and perhaps have to restrict notifier rights to prevent mailboxes being spammed once with stupid threads and again with people leaving stupid threads. Once you have left a thread though it's done don't complain about the mail you get from people leaving threads just leave them yourself, or talk to your guild notifiers about not creating stupid threads. Most guilds need 5 for communication... Trade, GVG, GBs, In game Chat, random stuff... random is probably not needed but there are loads of other fp chains etc that aren't as key and players, for multiple reasons, may want to opt out of.
While it is still early days after initial frustration I have left the threads I don't need and am having no issues, I have made a suggestion to improve it in another thread to ease the transition between threads for new players arriving and leaving.
Sorry that was really long.
The new system has potential to be better than the old but unfortunately the developers appear to have selective hearing with regards to the problems and no respect for the live server customers who they consider to be extended beta players.