I will say the recent small patch has in fact helped for the GDI side in that the GDI Sandstorm spam can be countered more effectively by GDI Zone Troopers and Nod Cyborgs without them getting absolutely wrecked by the barrage of missiles. They currently now after the patch are much more manageable and cost the same as another of their counters being the GDI Titan.
Balance issue I am experiencing now is that after facing the Nod Rockworm it definitely needs to be toned down a bit, it is supposed to be roughly the Nod equivalent of the GDI Titan but it does not not share the same cost as the Rockworm costs 120 to the Titan's 130 cost. The main frustration that comes from this unit is that there is no way to intercept it on its route and swarming it with anti vehicle infantry as GDI or Nod tends to not end well as it punishes you anticipating its location by doing AOE damage to all units when it emerges, after which just a swat or two is needed and it has killed the squads send to deal with it. Also even if ambushed successfully it can rapidly reburrow to reposition itself from a mistake which to me makes no sense as without a way to damage it while moving this would make air the best way to deal with it as they don't take damage when it pops up and it can't attack them. However the problem is while Nod gets their Banshee early the GDI Orca and Kodiak are epic class units with the later being an epic unit meaning that GDI outside of Zone Troopers, Missile Squads/Jump jet Troopers cannot efficiently deal with the Rockworm if they lack the GDI Orca or Kodiak.
Now that also brings me to my next point in that I also feel the GDI Orca is also in need of some sort of nerf, as currently you can rush helipad and GDI Orca fly it to the enemy harvesters fire a volley, retreat to reload then come back for an easy harvester kill that can you repeat and usually decides the match since you just wrecked the enemy player's economy with one unit. It is also hard to destroy unless you are specifically running the GDI Talon to counter it as it is a Fastest speed unit. It also wrecks the GDI Pitbull a little too hard being one of GDI's anti vehicle/anti air units, along with the GDI Wolverine another Anti Air ground unit. Possible nerfs could be to either its damage per missile or its reloading time in between volleys.
Final balance change that should get some sort of address in the future is that GDI currently has horrible time dealing with any of late game infantry units such as the GDI Zone Troopers, the Nod Confessor Cabal and Cyborg combo as they lack any sort of dedicated anti infantry unit like the Nod Flame Troopers and Chemical Troopers, while GDI does have anti infantry tech lab units in the Wolverine it tends to lose against the above combo as the Confessors boost the Cyborg's attack speed allowing them to shred the Wolverine. The GDI answer to this of course would be the Disruptor Tank unlock but that comes at level 10, mean while Nod starts out with the answer against this combo with the Flame Tank or at level 6 they get their Flame Troopers which can toast the Cyborg meanwhile GDI's only answer to this combo would be to throw Wolverines and Rifleman at this combo unit they manage to break through.
There is of course the GDI Sniper Teams which I being Level 8 have yet to unlock but I do recall JadeXyan mentioning that they are nothing more but gloried Rifleman Squads with slightly better Health and 2+ tile range with worse damage than said Rifleman at 5x the cost! This to me makes absolutely no sense considering Nod's Flame Troopers are 4x times the cost of the Nod Militants but with superior Health and DPS against infantry which they get earlier then GDI's Sniper Teams which are not only bad stat wise but come much later in the unlock for GDI. The solution to this is to either reduce the unlock requirement for this unit to that of Nod's Flame Troopers which is Level 6 or buff their stats to that of the Flame Troopers along with a slightly reduced cost to make them even a consideration to be used over Rifleman Squads.