I suggest adding different color options (at least 5) for e-mail flags so you can choose the importance or urgency, or any other category you choose, for emails. Having just one color flag gets very busy and confusing very fast. I have a tons of flagged emails and do not know which is which. Some are personal, others are related to my website (#1 on Google so busy), some are WordPress related, some related to my eBay listings, etc., etc. Maybe 6 different colors for flags, letting the user decide what the colors are for. Or give each custom Folder an assigned color like Outlook.
I'm not sure what kind of email system you use, but it kind of sounds like you might use workspace. Although we don't have colored flags yet, we do have message highlighting. You can use this to color code incoming messages automatically. If you have Office 365 you can use color categories to organize your inbox. I hope this helps!!
To have different color flags would be excellent. The problem with message highlighting is that it's automated. There are two of us monitoring this email now (workspace), and we would like to individually flag/color emails for each other as necessary, so using one-color flag or a highlighting rule doesn't fit our needs.