I'm not a big fan of the t1 crappy unit - t2 awesome unit dichotomy. I think t2 should be more about support and special abilities than a straight upgrade. And then t1 can be buffed to the level of t2 T2 tank should be replaced with a much more expensive bigger sized model. Super-tank with special alt fire abilities T2 short range tank - temporary speed boost with cooldown. T1 long range tank - weaker version of commander weapon.
And that's the way it used to be all the way from Ta through Supcom to Pa. Devs have made it this way and it would require to much effort to change it in Pa. Is it a bad mechanic? Don't know, but I know that a mechanic that you are suggesting would encourage more the use of t1 in the late game as t2 would be units for a more special cause and therefore used less frequently. A game would be more about t1. Another problem is that in games like Pa to many special abilities just don't fit or there are not enough of the ones that will fit. You are not going to make starcraft out of it. What special abilities can there be for units? I can not think of many, unless you mean something like: speeds up units in the area, increases range, buffs damage and hp, gives a burst of emp that temporarily disables units. This encourages micro to much. Supcom 2 whent in this direction and trust me the game was a disaster.
I am against the idea of common units having alt fire capabilities. It promotes micro gameplay. Also. We don't have the full unit roster. There will be some Advanced units that are a direct upgrade of basic units. That is something the devs have said and it's a good thing that some of them are. The devs are going to be adding more units that aren't direct upgrades.
I don't mind direct upgrades, as long as there is a viability in having larger number of weaker units instead. If not, just make sure you get to the T2 before your opponent
T2 is superior in every way conceivable, and they are more cost effective. There is no viability in having large numbers of them. They also cannot kill turrets.