I have used other CRMs (Copper/Prosperworks) which treats emails differently than Hubspot. It is better in some ways and not in others. Where Copper is better is that is sync in emails from Gmail and can pull in historical emails on contacts which can be helpful if there are important emails prior to adding the contact in Hubspot or prior to when a user was added into the Hubspot CRM. In addition, it synced all emails and all emails related to a contact were automatically associated to a deal in which the contact was associated. This ensures that all emails are searchable in a deal. At the moment, Hubspot requires emails sent to be tagged to a specific deal and limits the amount of deals it tags emails to (5 most recent deals). The prolem is this can cause some emails to be missed/lost if a user does not tag them correctly or forgets to. It also has the issue of inbound emails from the contact to be auto tagged to only the 5 most recent deals which may or may not be correct.
In the end, I think it is best to have an option to sync email in the same fashion that Copper treats emails. The trade off being all deals will show all emails for a contact, but with the benefit that no deal will mistakenly be missing an email.