After countless failures with the "kill all probes first and then all cube at the same time" method, I can only conclude that it is the wrong tactic. Sure it *can* work inconsistently, but it *rarely* works. Now a million people will respond with "Nuh-uh! We do it in our Private Teams of all Borg fitted Escorts all the time!" I humbly suggest that any heavy DPS private team is going to be successful at any map in the game almost without any other strategy.
The simultaneous destruction strategy was aimed at teams with a good ability to coordinate, whether that is simply because you have experienced players updating the team with the health of every cube, voice comms, whatever. It's a strategy that works, and at the time the guide was written the most effective tactic. I'm the one who wrote it, and even I won't say that it's the best strategy, but it does work consistently if properly executed. I've updated my guide with a few more pug-friendly tactics after reading what people have had to say in this thread however. Check it out.
As always, if you have suggestions for improving the guide, please head over there and post. If you think you have a better tactic, tell me about it and I'll consider adding about it, don't just keep it to yourself or a single thread in the PvE forums where it won't be easily found a month down the road.
Personally, these days I don't use any sort of fancy strategy myself; I just go in with my PvP fleet / team and we slaughter everything with eight+ minutes to spare thanks to great DPS and cross-healing to keep everyone alive.