TA2 should take place before TA. This would be the time when the Arm and Core armies were at their prime and cities were new. Units would be better and stronger and more available, unlike in their shattered and devastated future.

A larger unit limit than 500.

The ability to build bridges.

All features on a map should be destructible.

Units, trees, and buildings should all be made to scale.

The AI can build nukes and anti-nukes that work.

The AI is smart enough to use radar and sonar jamming.

The AI can use transport units in skirmish games.

The AI can use construction units to assist its factories that are building units.

The AI no longer sends every unit to one enemy location.

The allied AI can talk back to you about an enemy it has found.

Allied AI's can share mapping and radar info with you.

Terrain can become cratered during battle.

32-bit graphics.

Unit formations.

The AI is smart enough to use resurrection units.

The AI is smart enough to capture player's units.

Add a third race? Well, maybe just have humans running around in panic when their cars and buildings are blown up. Maybe have humans running around in factories (getting themselves cloned?) while Arm units are being built. Veteran (as well as non-veteran?) humans can eject from damaged Arm units and later board new or repaired units.

Seamless in-game storyline that uses the gaming engine to tell it.

Add voice communication.

Damaged units move slower.

Damaged units have parts missing.

Weapons should have more logical units to target. Tanks shouldn't be targeting underwater bases like they do now.

When half-submerged enemy units are aimed at, torpedoes should aim for their bottom half and all other weapons should aim for their upper half. Not the other way around.

The ability to record battles and upload them for others to watch.

More realistic unit armor damage and unit critical hit results.

New buildings become damaged in battle and end up looking like the shattered urban buildings we were used to seeing in Total Annihilation: The Core Contingency.

The ability to save the map being played on in its current state (with newly battered buildings and craters and all) for use in other games as starting maps.

A new map option that allows areas of a map to go black again when your units no longer occupy them.

Water tides that rise and fall which affect ground and sea units.