Dawn of War and Company of Heroes both have squad-based infantry units. You give commands to the squad as a whole, rather than individual units.
However, while this is better, it's still not
great. And I don't feel that machine-only games are "fixing" the infantry problem, they're just avoiding it because they don't know how to make it work.
Dawn of War (and CoH, since it used a similar system) did indeed allow for infantry units later into the game. The difference is that in Dawn of War, there were units classed as "infantry" who could easily take on most tanks in a head-on fight. Even the more standard units had such high durability that they could withstand a heavy amount of vehicle fire.
CoH, on the other hand, tried to model realistic infantry and tanks. Since they didn't provide all the tactical advantages of infantry (they were better about it, but still not quite there), the fleshy footsoldiers were quickly outclassed by tanks. Infantry are only used in the early game, as flag-grabbers and rush units. Later, it's the vehicles who take over, with the only footmen being engineers. Maybe some mortar teams, if they're into that.
Actually I like the idea of automated infantry, but I feel we need it for all units. The classic RTS is hugely unrealistic in that on one hand you seem to command the whole battle, but on the other you have to command all your individual troops. In real life there would be 2 levels of command between those things, but in the game- it's all you.
This is also one of my big beefs with RTS games, and sort of what I'm getting at with the automated infantry. However, I don't know how many people would play a combat-based RTS where you didn't get to command the troops directly. That's why I left in the option of being able to issue direct orders to the heavy armor and support units.
A Majesty-like system might work, but Majesty was also a lot about maintaining your infrastructure. For a modern war game, I'm unsure as to how you could accomplish an involved gaming experience without having to command the troops. I don't know what all sort of management would be involved with military bases.
It could be pulled off, and thus push the focus even more into the strategic planning field, since you'd be working out the best place for another base or what direction you should push production into, rather than telling that tank to start backing up and switch targets to the heavily damaged vehicle that just showed up, rather than the enemy tank it was previously plugging away at.
Hmm... Might have to think about that a bit.