I agree with most of your points, but not with your execution.
I think we went wrong in all departments, from the selection of our squad, to the selection of the team XI, to our batting line-up, to the bowlers we chose to bowl at the time we did. Dhoni can be blamed for much of this, but he can't be blamed for the poor bowling. I'm sure Dhoni didn't ask our bowlers to bowl as many long hops as they did in this tournament.
Fatigue is one thing--the IPL being as long as it is. It's supposed to get even longer, right, with 2 more teams added? But reading Sidharth Monga's article, it appears that we don't just prioritize this tournament at all. We just kinda show up and see how it goes. When we won back in 2007, the tournament actually meant something to us because we had been knocked out by Bangladesh in the World Cup earlier that year. We, along with Pakistan, were playing for pride. The last two editions of the tournament have seemed like a postseason for the IPL and our players just don't have the intensity or desire.
This is not squarely fatigue, though... well perhaps mental fatigue. For example, when Dinesh Karthik strode out to bat against Sri Lanka yesterday, you could see a stark contrast between his body language and that of most of the rest of the team. He was playing with intensity... like he wanted to win. The others were just kind of going through the motions. This was evident later in the day when Karthik pulled off a nice, flying stop at the boundary to prevent a four. Comparatively Yuvraj, Raina and Yusuf all had simple fumbles and misfields that led to runs.
We can take solace in the fact that we've still got a good Test batting line-up that should keep us competitive in most series'. However, once Tendulkar, Dravid and Laxman begin their retirement cycle, will the newcomers be able to come in and play with an intensity even when they're playing away from home? It took the Indian team with Dravid, Tendulkar, Laxman almost a decade before they got comfortable playing outside the subcontinent. We cannot afford the same incubation period, with all the top Test teams so closely bunched with each other.
The need to produce a decent fast bowler is a problem that we haven't been able to solve frequently enough to suggest that it just may be a physiological disadvantage we have. Changing the pitches may help encourage kids to become fast bowlers, but can the public really stomach the home series' losses that are bound to follow immediately after? I doubt it, very much.
In conclusion, this was a pretty apathetic outing by the Indian team, and ironically, I hope it was because of the IPL. Because there is not going to be any IPL before the Australian and South African tours this year so hopefully we'll be able to concentrate on the game better.