It's been a while since I re-read the earlier chapters, but my last feelings towards Archanphel were of pity as it was the cliched Frankenstein story whereby the Advents created a monster, but then abandoned/try to destroy it.
The fact that Archy saved the earth kinda suggests that he is a being of good nature, but his hatred towards those who created him sent him on a revenge trip. I think this was why he continued to create the 11 zoalords and build an army.
From the reaction between Arch and Apollyon, I think it's safe to say that he knows his identity and they share some trust/common goal. Whilst he may not approve of what he's doing, (removing the council of 12) it seems to me that Archy has acknowledged that this is necessary for the next phase of Arch/Apollyon's plan. Personally I still think it's highly likely Apollyon is Murakami. It would certainly make sense in this context.
As far as the next phase of the plan, I assume this requires the power of the zoacrystals, which is why Apollyon is collecting them. Whether it is to restore Arch's power/create new zoalords/create a new weapon/power the ark/simply destroy them I can't tell yet. He has 6 of 11 so far (if you include Guyot/Imakarums) and it's suspected that those still alive and loyal to archy are being spared, (Barcus and Shin). The 2 rogues will likely have theirs taken following the battle with Agito, leaving Galenos as the only real question mark.
I'm expecting a big reveal chapter on Silha with the Sagwa's reuniting with the Guyver team and Apollyon and Archenphel explaining their plan. It will involve the guyver unit/the crystals/the ark and the Uranus and both the operation and threat will be BIG!!
This is probably all still 5 years away though! lol