If I remember correctly, originally email alerts were not included because there was concern that it would be too much of a load on the old shared server we were on. We're on a much better server now, so it might be something that is added at some point.
If you ran your own webdip server, and had someone familiar with php, you could add email alerts yourself. There is already code in there for sending emails as part of the user registration process, so using it for email alerts should be fairly easy.
As for the unit colors, that is often a complaint of people new to webdip. But you get used to it. The color behind the unit indicates who owns the unit. After fall moves and spring moves for non-SCs, the territory's color is changed to whoever is in it. For SCs after spring moves, if the player who is in the SC doesn't own it, there is a colored box behind the unit that indicates this.
In my opinion it works quite well. My only issue is that often during the retreats phase, I'm looking ahead and forget to account for the dislodged unit that hasn't retreated yet and so doesn't show on the map.
The other thing to be aware of is that failed moves and some other stuff doesn't show on the small map. So always check the big map to see what all has happened after each phase. There you can see failed supports, failed convoys, and such.
My first diplomacy game was done by email at my work in the 90s. Would have been nice to have webdip way back then instead of having to have one person be the game master and not get to play.
Have fun!