RTS have so many problems but the core:
The AI is just... well... it sucks. There is no way to say it nicely, the AI derived for RTS are so far below the learning curve it isn't funny. Units are just too damn stupid to operate efficiently without human interaction. I can't even leave defensive positions without them forgetting how to shoot at enemies! I kid you not. At times I have had to point out to my defences that you don't have to wait till the enemy is within half the effective range before you start opening to fire. That it would be possible to lob shells at them at maximum effective range and achieve the same thing before they get close enough to fire back.
Ok, exaggerating, but not by much.
Then you have movability issues. There is nothing more frustrating then military manoeuvres, and that is in real world! For every command to move from A to B there is a small army of clerks and logistic officers who figure out just how to do this marvellous act. Well in all RTS your the head of command, giving the orders, but... you don't have any logistic officers period! This means, again, you need to micromanage every little action of every person in your troop if you want them to do what you intend. That you can't even assign them to a group and expect them to function as one, which you think would be a reasonable expectation. Your units will NOT be able to work out how to move without exposing themselves to unneeded enemy fire... or even how to figure out the best order to walk through a bottle neck! Even when you assign a formation, in games that allow you, it is more a exercise in AI futility as you can not expect them to hold formation and move at the same time without some really big screw ups.
It is move in a straight line between way points as fast as you can and screw what might be in your way.
This effect means whenever you move a group of units it always seems the units with the most armour, heath and able to punch back end up all the way at the back of the column. At the front? Your lightly armoured anti-air units think for some reason why can successfully storm the beaches of Normandy by themselves. Then of course your big hitters all get blown up by the lightest of enemy anti-ground aircraft now they can't defend themselves...
So on and so on.
If the intelligence was better the whole realm of RTS games would be strategic and even better to play. If each unit could figure out how to respond to an assault appropriately, without it either being standing around doing nothing or blindly following into ambushes, it would be nice. If they could figure out how to manoeuvre over terrain without either becoming stuck in the bottle necks or exposing themselves to needless destruction by sending through the easily destroyed units first I would be happier. If they where not so damn stupid I have to watch every unit then maybe we would see less mass-spamming of a single type of unit, cause at least you know all those units are going to be moving at the same pace.
But hell, this lack of intelligence has been the only 'real' challenge to overcome with RTS. If it wasn't for the fact you had to micro manage all your units the computers lack of understanding military tactics would make even the hardest setting boringly simple. Already it is too simple to figure out that they will always attack in style A or down path B. Removing the fact I have to watch path B, defending against attack style A while carrying out my own invasion force C, all simultaneously, would make the game so simple.
Mass spamming seems to eliminate a good chunk of the bad AI problem, maybe cause they all move at a given pace and are able to overwhelm the enemies defences if they where not designed to repel an attack of identical clones.
PS: Even the RTS games that have decided NOT to do the arcade system of C&C or starcraft, and focused on large scaled battles with well balanced units all have this same AI problem and it sucks. These ones are more strategic but without the means to ensure all you have to deal with is the macro level planning they fail in all the same places. Doesn't matter if you have a dozen types of tanks to choose from if all the damn things keep getting stuck in bottle necks and blown apart by a single enemy sitting a inch out of their effective range. All while your too busy making sure the anti-air don't out pace the tanks they are assigned to defend while trying to get them into position to pincer attack as well.
Only differences is these non-arcade style RTS is that you are allow you to suffer from AI related failure over battlefields measuring 100's of square KMs.