Interface in general is a major and under-appreciated aspect of RTS games. When a game lacks a great interface, people know it's bad, but seldom pick out that problem. When the game has a good interface, again people can feel it, but they rarely single it out. I believe a good interface is definitely among the very most important aspects of any game.
Much like gameplay or theme, this is something that cannot be addressed in a single topic, hence I will focus on something more specific: hot keys. Some people might laugh at this point, and wonder if I really have a whole topic worth of discussion just for hot keys. To such people I say: you clearly don't know me very well.
Easily overlooked by beginners to the genre, they make possibly the most accessible and useful parts of the interface. There's almost nothing that shouldn't have a hot key. Here are some of my recommendations for hot keys:
1) similar skills should share the same hot key. The idea here is that two units which share complementary or very similar abilities should share the same hot keys for those abilities. It's very helpful if all healing spells share the same hot key (warcraft III used the hot key "E" almost exclusively for all healing spells, which turns out to be very handy). If one unit has a spell that increases a unit's vulnerability to fire, it might be very useful if it shares a hot key with other fire spells (after all, I may want to use it, then quickly use a fire spell. If it's all the same hot key, that's very convenient!).
As I fully expect each race to fight differently (that is, swordsmen should have a somewhat different role for elves than they do for men, and likewise for orcs and dragons), this doesn't apply so much to barracks and other structures that produce units.
2) hot keys should keep to the far left side of the keyboard, and use as few keys as possible for as many abilities as possible. The idea here is that my right hand is always on my mouse, so it's difficult for my left hand to reach keys like "I" or "L", so don't make them hotkeys. Go out of your way to use some like Z, X, Q or W. These are easily tapped by a player on the go. They may not always be intuitive, but they're well placed buttons and if they're predictably used for similar abilities as in point 1, the standardization can be appreciated even by the most casual of players.
If implemented in conjunction with my earlier point (1), it's actually amazing easily to guess what the hotkey an ability uses. If there are only 5 or 6 commonly used hot keys, and you know the key used by other abilities of similar function, it's easy to deduce what the hot key must be. In fact, in some well designed games I often gamble on a hot key I don't even know - without looking - and get it right.
3) number groups ("control + #", I'm sure you've already got that implemented as it's very standard fare), which are encompassed by the overall category of hot keys, need to be flexible. I find one issue that often prevails is that units can only be a member of one group (that is, if a unit is part of group "1" and it is assigned to group "2", then it is removed from group "1" when this happens). This is most noteable when you have a large army that you want to move together, but in the heat of battle you might want to pick out specific parts of that army. Although I haven't seen all your interface, another big one would be healers. I may want my healers to exist in multiple groups for easy targetting.
Another issue with number groups is difficulty "merging" two groups. Sometimes, I may want to command both group 2 and group 3, but selecting both simultaneously is a real hassle when units are all mixed up on the battlefield. Normally in RTS games, holding shift means that any new units selected are added to the current group of select units. If I'm selecting a knight, and hold shift while selecting a wizard, I should be selecting both the knight and wizard. Likewise, if while holding shift I click both 2 and 3, I should have both groups 2 and 3 under my command. It's just a logical extension of the basic case, yet too often it's never implemented. This one isn't needed as often, but it's rather important none-the-less (plus it's intuitive).
4) make certain there's a hot key to toggle between unit types you have selected. This is called "sub-groups" in warcraft III, and it is one of the lifesaving features of its interface. I feel it should be a standard of the RTS genre. Essentially, if I have two types of units selected in one group, I can press 'tab' to alternate between their ability cards.
For instance, if I have priests and sorceresses selected, I can only see (and use) the spells of one type of unit at any time. By pressing tab, I can alternate which type of unit that is without deselecting any of them. The applications are varied. I can quickly activate a special ability on all of one type of unit without deselecting my army. Or, I could quickly active spells one all my heroes without deselecting any of them (along with other hot keys, this can allow for very rapid ability usage)
5) I feel this point is going off on a tangent, and could even merit its own topic as a result, but I'll say it briefly here: I feel that most RTS games fail greatly when it comes to their tutorial. People can figure out how to make units move and make them patrol, but you save them a lot of hassle if you teach them how to use a hot key to quickly give orders. I feel that the focus of tutorials in almost all games is very wrong. I see thirty minutes spent on moving units and telling them to attack when three minutes will suffice. Condense the tutorial down and try to cover as many topics as possible, and certain hot keys should be one of them.
A great way to test if a player has learned how to use hot keys is to make him use three special abilities in under a second. It's not possible if the player is only using a mouse, but using the hot keys it's easy. I think that's a great demonstration of their power and usefulness to a new player.