Sorry about the profanity.
I was thinking about some more things TA did right while in class:
Build queueing - In every RTS before TA (that I know of), each unit had to be clicked once it was ready to build (Red Alert), or had a very small queue (Starcraft); in Total Annihilation the queue was limitless. You could queue up 100 tanks for example, so you didn't have to keep coming back and reproducing them. This gave you a lot more freedom to spend time having fun (in battle), instead of having to constantly perform the tedious tasks of pointless macromanagement.
Resource management - The way Total Annihilation approached resource management was truly unique. In games before, you had a static amount of resources which could be used to make a static amount of units. In Total Annihilation, you could queue up limitless amounts of army and buildings, because the system was income/outcome based, meaning that you could plan to build things even before you had "money" in the bank. Once again, this allows the player more time on the battlefield, and less time in the base.
The Commander - TA was the first RTS game to introduce "The Commander" unit, which basically acted like a hybrid of the King and Queen in Chess. It was like the King in that if it died, you lost, but like the Queen in that it was your most powerful piece. The commander, though fairly slow, could build faster than any other engineer in the game, making him a powerful economic tool to have in your arsenal. He also had a fair bit of health, making him a good "tank" in an offensive push, perhaps turning the tide of battle by absorbing shots for your other units. Most importantly however, his main weapon - The D-Gun, and also the most powerful weapon in the entire game (kills anything in 1 shot), is what truly defined him as an awesome and unique force; an army of one.
Metal Corpses and Environmental Features - TA was the first game in which your units left realistic "corpses" when they died, impeding the path of units trying to get around them, and also being a source of extra metal when reclaimed. This added a brand new dynamic to the game that had never been done before, and was a major consideration when attacking or defending. For example, when attacking in Total Annihilation, if the attack failed, not only did you lose all the units sent in the attack, but ALSO gave the opponent a ton of free metal in the process. ;p Things like rocks and trees (environmental features) could also be reclaimed into your resource banks, which opened up some pretty cool economic options.
In the expansions they actually added "City Maps", in which the players battled in ruined cities, where every car, light pole, and building could be converted into another part of your war machine; pretty cool.
Defensive playstyles - Most RTS games force you into an aggressive role (think Starcraft where there are few defensive structures, and to win you HAVE to send units into your opponent's base). However, Total Annihilation offered defensive players ("turtles", as they were called) something too. The defensive structures in Total Annihilation were much more cost-effective and powerful than in previous RTS games, meaning you could make a fairly impenetrable wall of structures to take on a never-ending horde of enemy units. Corpses also helped in this regard because the more the enemy player died in an attempt to destroy you, the more the corpses of his own units became an obstacle. Also, Total Annihilation offered you the ability to turn 1 resource into another, creating a powerful, self-sustaining base that wasn't possible in other games.
So all in all, Total Annihilation offered the RTS genre something so ahead of its time, RTS games today are STILL struggling to catch up with all the innovations and features it brought to the table.