The bottom line was that everyone was concerned over the loss of Welker (not saying that I agree with him leaving b/c I don't, at least not over the small amt of money that was involved), and the loss of Llyod.
Amendola has looked like he belongs and has developed a nice chemistry with Brady. At this point Belichick took a gamble on a younger player who potentially has a higher upside over the course of the next 4-5 yrs, so we'll have to live with it. The talent and chemistry looks to be there. The main concern is the injury history, which can't be predicted for the future.
Thompkins actually seriously looks like a possible upgrade over Lloyd, who I'd have been fine with keeping as a WR3 or WR4, but never wanted to retain as the WR2/outside receiver. His talent, speed, etc were definitely limited. Thompkins looks as though he can come close to replicating Llyod's statistical production, while even upgrading some of the things that he failed at such as YACs and beating man coverage.
The other question was how to replace Hernandez---and although that will be tough, it appears as though they'll call on the next man up and go from there. Sudfeld + more of a running game can help to offset that loss.
In the end they may have a definite learning curve, but there is potential to be improved in certain areas too--or at least on par with last season, 2011, and 2010.