At first glance, a damage upgrade on Alpha 2 seems a bit much. About 6 or so of their machine-gunners will rip anything apart unless you got about 2 repairs on one of your units (I kept the towers the same, though). Did not test Alpha 3 yet.
I guess it depends on what there actually damage is at the end of alpha 1 what I had envisaged is that at the end of alpha 01 the player and the scav's machineguns would be the same in terms of range damage and fire power, then on alpha 2 since the player gets twin machineguns and the scav's don’t use them then they should get a small damage upgrade, because I would think that most players upon getting twin machineguns would upgrade there units.
with regards to the scav machinesguners ripping your units apart did you remember to account for the higher rate of fire when you boosted there damage slightly? because twin machineguns only have about half the rate of fire of regular machineguns so a full damage upgrade in conjunction with the higher rate of fire is probably why you where seeing the results you saw where bout 6 of there units would rip yours apart. So maybe instead of giving the scav's machineguns a full damage upgrade on alpha 2 maybe giving them half a damage upgrade would be more appropriate when combined with the higher rate of fire of regular machineguns doing that should should bring there regular machineguns closer to matching the twin machineguns.
Failing that you could always experiment with giving the scav buggies twin machineguns on alpha 02 to make them a little more threatening, i guess it depends on what is easer to do, but it's something worth experimenting with anyway.
As far as giving the scav's heavy machineguns I think the most fair place for that would be alpha 04 because the mission briefing warns us that the scav's on alpha 04 are more advanced than those on the first 3 levels and indeed we see this with the introduction of scav mini rocket pits so I see no reason that they wouldn’t also upgrade there machinegun units at that point, and again we can see how this players out in terms of difficulty and whither giving the scav's buggies heavy machineguns is to powerful, and maybe needs to be delayed slightly.
OK, sounds good. If we give the Scavengers the same weapons the Project have, we should also upgrade the Cannons of the Scavengers (BabaCannon and BabaBusCannon) to the Light Cannon that the Project will get in Alpha 05.
About the only minor problem I can see with doing that is that like for previous weapons I'm sure the player gets several cannon upgrades all in 1 go and I'm of the opinion that those damage upgrades should probably also be staggered just like the ones for machineguns and flamers but once we figure out were best to give the player damage upgrades for the cannons then I see no problem with having the scav's improve there cannons in line with the player, because obviously we are getting are equipment by stealing it from them and the new paradigm so its makes sense for there upgrades and the players upgrades to run parallel to each other, at least to begin with any way because obviously by the time you are finishing alpha 06 the player will be starting to pull ahead of the scav's in terms of technology and weapons, but of course than can be addresses by simply giving the scav's small boosts to there abilities as the player proceeds through alpha to make sure that scav's remain relevant, and again this makes sense from a plot point of view as the new paradigm would want to help they ally as they start to loosing to the project.