A big question you have to ask yourself is: How is the game going to play out?
Branching tech trees are an option. Everyone starts with the same things, and then make choices based on the style of play they will attempt. One of the key things when doing this is to ensure your maps and combat can combine to allow situational advantages depending on choices made. (ie, if user A chooses an Infantry focus tech tree, and user B chooses to jump into the Air tech tree, then make sure that User A can still do things like hide infantry in forests or buildings. Users must then try and force battle into an area that matches their advantage while avoiding fighting while their opponent has the advantage.)
Ideally a branching tech tree would allow baiting and feinting, make your opponent think that you are taking one route, allowing them to invest in a direct counter to that expected route, and then you ambush them with a context/location sensitive counter-counter. (A invests in Heavy Armour ground units, B invests in ground attack helicopters, and then A surprises B with a unit of AAA or AA Infantry hidden in a group of woods.)