That's actually a pretty good responce, because it is unfortunately all to true. It is maybe not the most helpful responce, but it is going to be hard to be helpful without writing the rules for you.
Basically, mass combat rules can be divided into one of two groups. Those that want the mass combat to take a while, and those that don't.
Every other interest can be seen as a special case of that.
For instance, some RPG groups don't often have mass combat in thier games, but when they do they expect to take a whole session (or maybe a whole weekend) to play the combat out in as elaborate and satisfying manner as possible. For this group, having the mass combat game be a game unto itself is fine, because it doesn't interupt play often and when it does it is a special occassion.
On the other hand, some RPG groups find themselves facing mass combat situations every time they turn around because the PC's have become lords and rulers in thier own right, with armies to command and legions of followers. After awhile, these groups are pretty much forced to abandon using a full blown resolution system for all but the most important battles.
Then again, some RPG groups don't want to do mass combat at all. They consider it tiresome and think it gets in the way of what they want to do which is roleplay. Nonetheless, the DM and players will occasionally find their RP has taken them to a situation where resolution of a mass combat would be 'nice' and the DM, if he had some simple system, would rather use it than 'simple' DM fiat.
And finally, some RPG groups would rather run detailed mass combats than anything else they could do and become engrossed in the moving of armies.
So basically, you have two choices. Quick and simple, or detailed and gory. Finding a balance between these two is very hard. Finding a balance that pleases everyone is impossible. Instead, you should strive to meet the goal of a system that can play out in X ammount of time, where X is a number convienent to some large portion of RPG groups. I'd say idea time frames are probably 6 hours, 1 1/2 hours, and 10-15 minutes. For each length, you'll find some large audience.
I've personally been involved in RPG inspired mass combats (using Battlesystem) that took up a two car garage, something like 6000 counters, and nearly 24 hours of continious play to resolve. Although there are some things about it that are ok, Battlesystem is in my opinion an example of what not to do.
Of all the attributes that you could have in a mass combat system for an RPG, the single most important IMO is scalability. Very very quickly an RPG campaign can move from needing the ability to resolve combats with a couple hundred on a side, to a couple thousand on a side, to tens of thousands on a side as epic story lines progress towards thier conclusions and PC power and influence grow.
Scalabilty is not easy to achieve. In a sence the only way to do it is provide several levels to the game and let the DM choose the one that best suits his needs at the moment and thats almost like writing several different systems.
Of course, the easy solution to scalability is to say that a clash between units of 100 or 1000 troops is identical to a clash between units of 10 troops. Problem is that it is not.
Most mass combat systems are enherently tactical and make tactical considerations the foremost or even sole consideration in thier design. That's fine for set peices that occur in a setting vacuum and involve relatively small numbers of troops (a couple hundred), and most players are going to want something that resolves X vs. Y when the RPG decides X vs. Y occurs.
But tactical games aren't the only possiblity. You can play games on a strategic or operational level. Some DM's, especially those running PC's who are rulers, are going to want operational or strategic resolution systems. As the number of troops becomes large, tactical considerations become almost a wash and can be reduced to a couple of mere numbers that indicate how potent the unit is tactically. What those DM's are ultimately concerned about is not only whether X unit survives to fight again, but also how much it costs to move X unit from here to there and whether or not the PC can pay for it and whether the army can support itself in the field if he can't. Operational level games are particularly suited to providing to DM's that need to arbitrate the outcome of entire wars but have no interest in setting down and resolving the scores of battles that take place in them.
Finally, a peice of advice. Don't produce supplemental information for the game before the game itself is complete (and a success). Don't worry about mass combat feats, prestige classes, spells, and so on and so forth until the system itself is complete and tested. You've got enough on your plate as it is.