I really like the microbial shroud proposed change. I had a few ideas: Instead of decreasing energy cost or increasing duration, make the effect larger. It makes the front edge flatter, and gives more chance for it to be exploited by the other player (particularly flanking).
Instead of having it affect buildings, have shroud obscure the ground from both players view, giving it more uses than just air defense. There might be banes, defend scouting, who knows what is unloading from the nydus or that a nydus is popping, or even just a feint. (If the alpha star team is up to the challenge).
Instead of increasing lurker range (with upgrade), have shroud negate air based detection. Spell (emp would probably need to reveal burrowed) and defensive structure detectors. Lurkers still attack, roach and infestor can retreat, other zerg units can burrow, be passed over, unborrow and thus have flanked.
Sorry to leave the primary subject, I have a few other ideas.
Instead of increasing the nydus worm cost, increase the cooldown. If the zerg want to constantly nydus, they need to build multiple nydus networks, increasing their resource commitment, but also allowing simultaneous worms. Perhaps even increase the cooldown greatly (like 3X) but decrease the cost of the nydus network structure. This would also encourage using the network to respond between threats in the zerg base (broodwar style).
Adept upgrade, have it increase adept shield armor by 2 (and allow recharging in combat or increase armor as well), as well as increase shield hp. The adept counters light units. Shield armor would make it more attractive for this role / differentiate it more from zealot.