SAAS means you're vulnerable to vendor change with every pageload.
Though there are getting to be tools which allow you to reverse-engineer sites and design them how you want, but this is subject to a lot of churn keeping up with the SAAS vendor.
True, but it would be nice to augment Mutt with things like tags and conversations[1] without having convoluted setups involving hacks with external scripts.
Another example, it would be really cool to be able to edit email as Markdown/Textile/reStructuredText and have it converted to a text+html (multipart/alternative) email, but currently there is no way to do that with Mutt without using some sort of sendmail wrapper that does this.
[1] I realize that Gmail's threading isn't 'true' threading, but I'm talking about pulling in the entire thread even if it's not part of the current email folder.
I used sup for many years (and contributed some very minor patches). sup is no longer maintained and it's difficult to get running with ruby 1.9. Some good people that weren't happy with sup created notmuch (http://notmuchmail.org/) with similar goals. There is a mutt fork that uses morning called mutt-kz (https://github.com/karelzak/mutt-kz/wiki).
I'm not as satisfied with mutt-kz as I was with sup, but it's probably even better if you have invested a lot of time configuring mutt just so.
SAAS means you're vulnerable to vendor change with every pageload.
Though there are getting to be tools which allow you to reverse-engineer sites and design them how you want, but this is subject to a lot of churn keeping up with the SAAS vendor.
Still lovin' my mutt.