Wow... Camate... I suddenly want to finish leveling PUP.
As a side note: Activate/Deactivate is an accepted strategy? I never would have guessed the Devs were ok with this -- I thought it was just something they overlooked.
With regards to the Silence issue.
its not that they cast on monsters that resist it -- they will cast it on a monster that has no spells, but has MP; such as Crab.
No one has any complaints with abilities being resisted -- that happens, and while its unfortunate, its no worse than a missed weapon skill. The problem is when the automaton wastes its lengthy casting cycle on a spell that has no purpose or effect whether it hits or misses.
Separating out the magic types (Dark, Elemental, Enfeebling, Healing) and giving each its own timer will help this, but its still something that should be looked into.
The problem isn't maneuvers, the problem is that maneuvers are pet abilities. There shouldn't be an animation attached to the Puppetmaster. The Automaton, when activating a maneuver, should get that little steam animation from the PUP special emote (as a kind of "kicking into gear" indication) so that it doesn't distract from the PUP's attack cycles.
The Auto deals most of the damage, but the PUP's ability to maintain decent DPS is pretty important too. In situations where the automaton is just nuking, losing DPS because you have to freshen up your maneuvers hurts the PUP overall. Maneuvers don't need to be fixed, the annoying animation just needs to change.