The problem with Williams IMO is Sam Michaels. Williams in season development always stagnate. This is a case of leadership and directing the limited resources into improving the car efficiently. Force India did not have tons of money to burn, but they did a better development job than Williams. Why? Because the employed Mclaren processes in identifying the priority areas when developing a car. The Williams started the season a top 3 car and come the end they were nowhere. Something is wrong somewhere, and you've got to look at the top for the answers.
As you mentioned though, they do have limited resources. Force India, let's not forget, started with a much lower baseline than Williams did this season, so of course it was easier for them to improve the car (I'm not saying that FI didn't do an exceptionally good job by the way). The FI was also only fast on some tracks whereas Williams was quick on all circuits.
As some have mentioned, Williams (like Brawn & Toyota) had the benefit of the double diffuser at the start of the season. If you compare Brawn's pace at the start/end of the season to that of Williams you'd have to say that Williams have done a better job at keeping pace.
Looking at Rosberg's performances, OK he scored less points in the second half of the season, but his qualifying pace was fairly similar (with his best quali result being in the second).
Nakajima too - although probably more to do with the driver getting more out of the car - actually had a much better second half than first half.
My personal opinion is that Sam Michael doesn't do a bad job, working on a limited budget they achieve a consistent (if not mind-blowing) level of performance. There is almost always a Williams in Q3 of qualifying, which is a good achievement and not one that you can purely put down to the driver otherwise Jarno Trulli would have done the same thing.
To my mind Willi's are doing a great job with what they have and I'm still proud to be a fan.