... Well, my brain is slightly broken here.
The wargames are very impressive, with Thundercracker getting the chance to really shine. His dealing with Runamuck was very nicely done, but his fight with Razorclaw was brilliant. The fact Megatron was planning/hoping for this development had the effect of showing a much smarter side to Megs then he usually gets.
Soundwave having an online identity cracked me up, especially as it let you show the side of his character we don't normally see is already there. The entire hacking arc was nicely done, with everyone getting the chance to be awesome. The followup in Little Iacon... You brought the Geth in, which worked remarkably well (Although I suspect they're obeying a different ancient evil robot this time), then you had Stinger, Sari, Bulkhead and Miko. The last one threw me for a moment, possibly because I'm only just starting with Prime and in the eps I've seen, she's rather irritating. Still, merging the Prime and Animated versions of Bulkheads is nifty, and she seems a bit better suited for the madness here :)
Then there's Starscreams return. No matter how I look at it, it was awesome. From landing the dropship, generally being amusing, and his scene with Alexis... Not only did you blend in elements of his Armada version, the choice of lines there now has me seeing him as the Raggedy Decepticon.
Loved this chapter, curious at the cliffhanger, eagerly waiting for more.
Matrix Dragon, J. Random Nutter