Here is the problem, and you can search and find lots of people who complain about it:
Let's say you sell something (e.g., run a small business selling on the Internet) and you use PayPal to accept payments. PayPal sends every single notification of a payment with the exact same subject line "Notification of payment received".
So, if you receive a payment from Bobby Sue, and then you get a payment from Billy Jo, Gmail shows:
Bobby Sue via PayPal(2) - Notification of payment received
and /nothing/ for Billy Jo. Billy is the (2), but it's buried in the same "thread"
And if you process Bobby Sue's order, and archive it, that archives Billy Jo's order as well. If you aren't careful, you can forget to ship anything for that order. And Billy don't like that.
I've searched long and hard for a setting or a way to keep Gmail from doing that, or to change what PayPal sends in its subject line. Seems to be a case of immovable object and irresistible force.
My only idea is that Gmail can be accessed by app scripts, and perhaps one could be written to find the transaction id in the email and tack it onto the subject when it arrives. But I can't find any example scripts that edit the subject line. Any idea if that is possible?