Please accept my apologies for going off half-cocked, I shouldn't have reacted in such harsh way.
As I see it, the problem with wargaming simulation and RPGs is that the miniatures seem to promote the idea that the moment you start running a war, you step back from the idea of simulating the exploits of a D&D party, and start simulating a wargame instead.
This is appropriate when the PCs are running armies and nations, but most games aren't like that. That's not to say you shouldn't have the option (Birthright analogues should exist, for instance), but it would be nice to see some more original approaches to the problem, such as a system designed to (a) deal with the PC's interaction with the war and (b) deal with the impact of the war on the campaign world. Instead, the default approach seems to be the traditional (c) - simulate the battle directly - in other words, a wargame.
tactical level...miniature free game
Miniatures are great for tactical gameplay, it cannot be denied...but even games involving large numbers of miniatures (e.g. Warhammer and 40K) still end up effectively only being skirmish battles, with handfuls of troops. Modern consumers don't seem to like games involving one miniature representing 10 troops. Using counters or pre-painted miniatures would alleviate the problem somewhat.
A pen and paper system would be indeed be inferior on a tactical level, as far as representing the clash of armies on a tactical level goes. For strategic, clash of nations, armies marching across the lands to do battle "over there" purposes, it would be fine - and most of that happens off-camera, anyway. You don't need to get down to brass tacks to represent (b), the impact on the campaign world...so it's appropriate in that respect.
As far as (a), the PC interaction with the war, goes, a system could conceivably identify skirmishes which the PCs get involved in if they get directly involved in the battle, or the outcome of the leadership decisions they make. If they're on the front line, or hurling fireballs from the battlements, then yes, they'll be getting attacked by waves of minis/counters, and the system will need to generate enemies and allies in the near range to fight - but on the standard d20 battlemap only, and not using a substitute for the d20 rules - use a proxy system, and players may well whinge that if simulated using real D&D, they might never have died. If they move to another part of the battlefield, the paper and pencil system might be able to generate what's going on there as well, add up the PC impact on the battle, and alter the flow of the battlefield accordingly.
Oh yeah, and it'll make you coffee and walk your dog too. Of course, it's a huge design goal, and might not even be possible, but it seems to match D&D campaign needs more than a wargame sub-game does.
With regards to combining RPGs and wargames, there are no limited army lists, so you'll need minis for all array of strange beasties and troops, or just be forced to compromise with proxies - thus the RPG mini battle probably won't look as good as armies built from dedicated and supported army lists. When you add to that the overhead of time and money a miniatures wargame consumes, combined with the time (and to a lesser extent, money) that roleplaying consumes, it will be interesting to see whether WotC's long term plan to turn roleplayers into wargamers as well (thus the intentional exclusion of mass combat rules from the DMG, so I read) is feasible. In the Warhammer hobby, modelling seems to come first, or at least, a very close second to playing for most folks.
I'll shut up now.