I think a plugin that would reload others but keep their settings would be cool. Where we could like click 1 button and it reload them all or we can check box the ones we want. I mainly need this for when uploading a new theme as of now anything that makes a template change will not load for new uploaded themes and if you have 25-50 plugins going in and deactivating and reactivating each plugin each time gets kind of annoying. If this is possible it would be great! Thanks
It's up to the plugin authors to solve this issue. Plugins don't have to (shouldn't) lose settings and other data when you deactivate them. The plugin can choose to clean up such things in the uninstall routine instead.
What you're actually asking for sounds like a settings import/export facility. Something that stores (exports) all settings, then deactivates all plugins and activates them again, then restores (imports) the previosuly stored settings. So any plugins that loses settings on deactivate would then be restored. It would also be useful if you wanted to play around with settings of your board, and then when you find you broke something, restore all settings to their previous values.
Such a thing could be done, but it would not actually solve the issues some plugins have. It would only work for settings, when plugins which lose data on deactivate also lose templates, additional permissions, custom database tables, etc. etc and there is no way for an external plugin to keep track of all those. In the end such issues ultimately have to be solved by the plugin authors themselves.
In a way, the settings exporter already exists... database backups! Make a backup of your settings and settinggroups tables, deactivate/activate all, then restore those tables, using phpMyAdmin or whatever. Afterwards go to any setting and click save so inc/settings.php will be regenerated also.