Mostly because I have multiple email addresses. But I make good use of the filters (which could be improved) and tags. That really helps with searching through everything.

If I only had one email account I probably wouldn't care as much but that's not as common these days

Juggling multiple e-mail accounts in a single client, and I haven't found anything better - also haven't really had any major complaints, the desktoo app works perfectly for what I use it for.

What alternative do you suggest?

On my desktop, because I download my mail, store it on my laptop, backup it. Nothing is left on the servers of my email provider.