> The main controversy was indirect, e. g. several actors - including Craig - trying to patent ESTs.

You're under-selling it. Celera filed thousands of patents on expressed sequence tags, long before anyone knew anything about them. It was a land grab.

Also, it only seems obvious if you're looking back at it with 20+ years of hindsight, but it was quite unclear at the time if it was possible to obtain a full read of the genome from shotgun sequencing alone. The human genome is 3000x larger than H. influenzae, and significantly more complex.