I was thinking, perhaps a mod could be made that has this fact at the heart of its design. For example, missile towers (defenders, punishers) would be almost flat, so that LLT's can shoot over them. (Guardians) would also still be low, because they can shoot over units; they would be about as high as an LLT. Then Heavy Laser Towers would be able to shoot over ALL the aformentioned units, with Annihilators coming in as the tallest defence structure.
What's interesting about this design, is that it means there is a reason intrinsically in the game that you should advance to a high tech level. Right now, the reason you get lvl 2 units is because for the cost, they kill lvl 1. However, this is very artificial - while lvl 2 units should be better for the cost, they shouldn't absolutely make lvl 1 pointless.
The nice thing about this is that a base without high tech lvl defences is at a severe disadvantage, but a base without low tech structures is, too.
It also encourages more strategic placement of structures, as well as forcing players to use terrain more efficiently, because terrain can elevate units just as their own height does. So a good player could work out what angle to attack from in order to have least exposure to enemy fire.
Of course, tech lvl2 units aren't always going to be bigger than lvl1, but the anomolies also add strategic opportunities.
Imagine an army of ARM kbot's - Peewees and Hammers. This army works quite well, because the Peewees make up the front line (another thing, peewees should have more life), and the Hammers back them up with artillery fire.
A mobile energy weapon (Penetrator) would be the perfect backup for this army. It can shoot over all those little units, but is still under their protection.
On the other hand, imagine an army of bulldogs. They are much larger than lvl 1 kbot's, so the Mobile Energy Eeapon would be difficult to use with them. Instead, you would use mobile artillery, which can shoot over just about anything.
But the strategic opportunities go much deeper than this, even. Imagine we have two beamlaser units; one is a Vehicle, the other is a Spider.
Now consider the map "small divide". The vehicle is awsome mobile defence on this map - any units that come over the mountain can be shot by all your tall laser units, as long as they are spaced properly. Conversely, the less cost effective laser spider can walk over the mountain, and every spider that is over, but still on the slope can fire.

A few more things to consider:
1.
I think all missiles should have high trajectory, just like artillery. Artillery should generally have more range and do larger area effect damage, but be less accurate, while missiles/rockets would be very accurate but suffer slightly less range and less area of effect. Missiles are also good against air, so they are not exactly the same with high trajectory.
Lasers should all be beamlasers. I'm sick and tired of lasers significantly slower than bullets. They should all also cost energy to fire, same as lightning.
That means that we need a basic weapon that does not have a high trajectory, and also does not cost energy to fire. So I reckon we use EMG and Plasma. Plasma would be kind of like artillery without high trajectory and with less range, kind of like the weapon used by Stumpy's. We could also use another 'basic' weapon or two, so suggestions are welcome.
2.
This is an opportunity for higher poly units to be sculpted! That would be really nice, you can't deny that. It makes a lot more sense for all that work to go into a new mod rather than just remaking OTA units.
3.
Dragons teeth of different heights will have huge strategic purposes, as will popup units. Just think - you build your popup lasers units in front of your artillery. Leave the popup unit on hold fire, and your opponent will no doubt try to destroy the artillery unit by closing the distance. Well, as soon as he does, get your popup lasers into the action and make mince meat of the opposition!
4.
Lvl 3 super units with more than three weapons would be very cool.
5.
Any other suggestions?