As a basic reply to your requests:
There is a [ + ] button when you add cards. It will add a new line to the current entry of the same card and let you choose new set/rarity/language, etc.
Expansion symbols could use some work, but Gatherer actually *does* have the older symbols color-coded for rarity: black, silver, and gold. It was a change they made for Magic Online and ported it into Gatherer for easy reference.
I am with you on the expanding the Expansion Sets. I have mentioned at least 3 (now 4 times) that they really need to remove "promo" as an add-on to a card and instead include ALL of the promotional Expansion sets that the cards come from including at least: Pre-release, Launch Party, Buy-A-Box, FNM Promo, Grand Prix Promo, Judge Promo, Textless Promo, Junior Super Series (aka JSS), Summer Magic, etc.
The prices are reflective of the TCGPlayer pricing, by the way. Unless you change it, the prices are based on the "average" price, but this can be set to use "high" or "low" if you like by way of your preferences. Some cards list for $0.00 due to error with either TCGPlayer or DeckBox.
You can see the total value of your collection while on your inventory screen by hovering over "View" and clicking on "Show Value". This only throws the value up based on your total cards. I could see a reason to exclude all your cards of $1 or less, and could be a neat add-on just to give a person a reasonable idea of what their collection is worth minus all the chaff. Maybe even make it scalable by value? Like, it gives you the option to exclude cards with value less than $X.YZ? Seems cool. Might be difficult for DeckBox to program as I think there are hundreds of other places they could utilize their time and energy programming though.
I *really* like the idea of being able to add a scan for a card that is unique. I have many "big ticket" items that I would want scans of. Of course, you can always scan them for anyone interested, but it definitely would save time if there was a way to have them uploaded into your inventory already. Great request! Don't know how difficult this would be for DeckBox, but one to keep in mind.