I actually really like the ending, except for the Catalyst. I feel like it would have been better to portray it as having gone rampant after millions of years, the Reapers' true purpose being forgotten even by themselves, now known only to the insane catalyst.
They were originally built to help organics defeat an army of synthetic enemies that was on the verge of victory. They turned the tide, but as new synthetics were built and rebelled, it came to the conclusion that organics were the problem. This would better explain their motivation, and Sovereign's incongruous dialog in Mass Effect 1.
