Changing the emphasis doesn't amount to much: if the FDA is not conducting, or compelling companies to conduct, sufficiently rigorous safety assessments prior to the marketing of a GMO product and instead presumes such products to be safe until evidence to the contrary arises, they are failing their responsibility to protect consumers. Of course the FDA retains its enforcement powers; my complaint is their being reactive instead of proactive.
Sorry if my selections were unsatisfactory--I didn't think /. would appreciate the whole text. My concerns then, in general terms, are:
1) The FDA permits companies themselves to make the determination of whether the genes introduced by GM are "generally regarded as safe" (GRAS). When companies determine GM modifications are GRAS (and I'm unaware of an instance they haven't), those foods are exempt from the food additive regulations.
2) Regulatory authority is, as you point out, split across the FDA, USDA and EPA. Each of the agencies only considers a subset of a proposed product. In the case of Bt potatoes, for instance, the FDA doesn't care about the Bt protein since it's a pesticide and therefore the EPA's problem. The EPA figures the original potato was safe and the Bt protein is safe, therefore the new Bt potato is safe. Interestingly, when it comes to labeling, the potato is back to being considered food and the FDA regs prohibit labeling of pesticides so Bt potatoes are anonymous when sold.
3) When GMO crops are evaluted, they are not done so with sufficient rigor. Consider again the Bt potato: the EPA supposedly tested the effects of Bt on mice but they didn't feed the mice Bt potatoes, they fed them pure Bt. If complications arose in the production of the protein within the potato itself, they couldn't have known.
How's that for process? Does the USDA do better? That second link you provided describes how the USDA 'streamlined' its regulations in order to "reduce the length of the petition process by more than 50 percent". I don't consider that an improvement.
Ultimately, though, you bring up the trump card: regulatory authority. I have no doubts whatsoever this will result in litigation which ultimately sees the ban struck down.