The PHC AI is absolutely crushing the Substrate now. They plow through them on a scale with putting one side on beginner and the other at normal. From what I can tell, it's almost entirely because they can't regenerate hull points effectively. I played some 2v2's last night with normal AI, and my tool Substrate partner rapidly lost every dreadnought it built, utterly failing to maintain any sort of force, rapidly losing ground once they were in play. Before Dreadnoughts, it was fairly effective in keeping it's footing, but their presence shifts combat from a slugfest between armies, to more of a mass obliteration game where weaker units are instantly eliminated and the only real staying power are the dreadnoughts. The PHC AI attack with full health dreadnoughts pretty reliably, but my Substrate partner kept losing them because they were fighting with half their hull gone. I finally managed to 2v1 the PHC and stick 3 dreadnoughts in it's base to keep it around, that was the only thing I could do for it, and it still couldn't affect the outcome even after I was babysitting it with three highly leveled units that melted everything they ran into.
Shields are nice, but not so much depending on the unit. With heavy repair/shield restore, a 10k hit point unit is 10k hit points of burst damage survival, that can be regenerated to full. All of the PHC methods of rapid regeneration target hulls, all of the Substrate methods target shields.
An 8k hull, 2k shield unit is effectively a 2k hit point unit under such circumstances. Every time it takes a large chunk of damage, it's stuck with this long lasting, hard to excise wound in it's overall durability, while a 10k hull unit on the other side is not. On Defense, this isn't too bad as long as the unit survives it's battle. An engineer or two can be stuck on patrol can clean things up fairly well, but engineers can't really be in combat, they don't have the durability to survive it. Single shots typically obliterate them now. Before when they had 100/100, they could stick around fairly often with a shield regenerator running. Putting a few on patrol at your choke points would keep your hull points in good order between battles, but they really don't work at all mid battle, and this is a significant management advantage for PHC regardless.
I'm 15 year past the days when I was top 50 material, arthritis, a lack of 17 hour gaming sessions, and a lack of interest in keeping such skills have all played their part quite effectively, so perhaps I'm missing stuff that fixes the balance at a high level of play. I can usually see the mechanical uses for things even if I'm not up to using them though, so I expect this is a bigger problem than just the Substrate AI being an absolute pushover. For the average yahoo, who will probably never even play ladder games, I probably wont myself, Substrate is an extremely frustrating side compared to PHC at present. Before that last patch, the super durable engineers and hilariously powerful maulers were evening things out pretty good.