v-serp: I have to say I think that one of the reasons everyone hates the matrix now is because Is0bel is such an atrocious decker. Her deck is just garbage, and her HP total is very low. With the Black ICs doing host damage, and her just eating it all, she gets killed pretty easily.
No I think most people hate the new matrix because it has crappy real-time "stealth" bits, crappy simple simon bits, and crappy memory games.
As you found out yourself, you were able to easily kick ass in the matrix with only a 5 decking - which would have been much harder in Dragonfall. This is another reason (related to all the above) why the new matrix is crap - decking skills hardly matter now. Those crappy Simon/memory games aren't even affected by decking stats!
While I dislike the new Matrix, it's easy enough to do, so I just power through it.
v-serp: I think my favorite team, especially for combat, is Gaichu, Duncan, Gobbet. But all the characters are solid enough. The game is pretty easy after all. I know they're adding more difficulty levels, I guess that's when we can find out what is actually viable or not at higher levels.
My favourites vary depending on the specialties of my main character. Gaichu for close combat, Duncan for ranged, Gobbet for support, Is0bel for decking and/or explosions.
Gaichu kicks ass, but he's best when someone like Gobbet is along so she can buff his accuracy and AP. For added fun, give him some Tokko so he gets more accurate/powerful every time he gets hit!
Duncan is to ranged combat what Gaichu is to close combat - so I tend to bring at least one of them along, sometimes both.
Is0bel might not have great accuracy, but her grenade launcher is still pretty cool. On the first play through I was a decker and still brought her along once or twice just for the launcher.
I also like Racter since many missions benefit from a drone. That and Koshei is pretty cool later on and/or when buffed with Racter's controller. It's a shame Racter himself isn't a great shot, but you can't have everything.