Money is a bit of a side issue, I note that Arsenal are not in that list yet they made it through a far harder group. On paper APOEL had a harder 3 teams to play (with Zenit, Shakthar and Porto (all have won the Europa League in the last 2-3 years) yet they didnt spend anything like that amount of money and made it through top of that group.
I think the problem is you (probably your manager) didn't take the opposition seriously enough this year. On paper the group was easier than other groups, but Benfica are reasonably dangerous team and have some talented players. Basel are not a team that will light up Europe, but they are well organised and hard to break down. Otelul were not great at all, but even at home you kind of limped past them without really convincing. Some of the players you used in the group stage (Macheda and Evans) are more like Carling Cup players, not really to be used in an active game of a CL (fair enough if you had qualified and it was the 6th game, but in crucial games they're too weak). For all Wesley Browns errors and John O'Shea criticism I think would have added a bit more experience to the back line. Smalling and Jones might become good players but their lack of CL experience left you a bit short. Ferdinand is a bit injury prone, Vidic had a red card and got injured tonight, you were left with Johnnie Evans as cover.
Good luck in the Europa League. 
(If you go for a centre back?)
