LOL this is funny. You probably consider these "major flaws" simply because you have never used an NVR or other vms and you dont realize how luck your are to have BI that allows this incredible fine tunning. I urge you to buy any alternative to BI and report back.
1) This is simply user error and failure to read the help files. The "major flaw" is a feature not available on any NVR and likely most vms.
However it IS available in blue iris. There are several ways to do this but the easiest way to do this is to simply limit push notifications to your own phone. This is explained in the help file.
"If you would like to send this notification to only a subset of connected mobile devices, you
may specify one or more “tags.” Separate multiple tags with semicolons. A mobile device
must have any one of the specified tags in order to receive the alert. Please see the Mobile
devices tab in Settings. Leave this box blank to send to all mobile devices."
IF you use text or email notifications simply enter your wifes info for that camera only.
IF you want to be able to toggle this function - again - easy, use profiles.
2) The mobile app needs work, but this is something that is no a huge deal. 99.9 percent of users are not constantly downloading video to their phones. More importantly you can do this via the browser on your mobile phone using ui3 - you will need to set begin and end times. The app is not needed at all...