My opinion -
Injuries: The ACL injury to Jared Warea-Hargreaves last season, and to Boyd Cordner in the off season putthe forwards behind the eight ball. It removed the two forwards who are the nominal leaders of the pack. Then add in the injuries suffered once the season started - Henderson, Copley, SKD, Tupou, Pearce (yes, he was out a few weeks injured), SST (yes he had an injury problem mid-season before the ACL injury last week), Lui - caused the team to be constantly chopping and changing. In fact the injuries in the forwards, which occurred when both Cordner and JWH were out, saw players brought in who were not up to first grade standard or who wee just not ready to make that step up yet. This constant chopping and changing prevented the side from building any chemistry or combinations.
Pearce's Suspension: This effected us as it meant we started the season with 2 relative rookies in the halves in Jayden Nikorima (who had played 0 NRL games) and Jackson Hastings (who had around 20 NRL games to his name). Combined with having a rookie fullback in Lartrell Mitchell, this meant we spent the first half of the season with an almost brand new spine. Coupled with the chopping and changing around them, it made it hard for these two players to settle. In fact it may have shown that Hastings was not as good as everyone first thought he was. Additionally I believe it lead to players like Friend and Guerra, as two of the few senior players available all year, to over play their hand in the game plan, which further caused disruption to the side. When their efforts did not come off it effected them negatively, Guerra in particular who for much of the mid-season hardly looked like an Origin calibre player.
Losing Roger Tuivasa-Scheck: This hurt more than Maloney as there was no real plan in place for this eventuality happening. Thus when it was announced he had taken the big money offer from the Warriors (which had we matched would have seen us lose quite a few players as he would have eaten up a lot of our salary cap to do e.g. Napa), the coaching staff were left in a scramble to find plan b. Latrell was not considered ready to be pitched straight into first gare at fullback, they wanted to blood him on the wing for a year first which is why they looked to Ferguson as the stop gap, but he didn't really fire so Latrell moved there after Round 1, but by Round 20 he was so beaten up physically, he was moved back to the wing so as to reduce the likelihood of injury, and Ferguson was back to fullback. What had been a position of real strength in 2015 was at best a "break even" in 2016.