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As we've seen with antibiotic resistance, expect Round-Up resistant weeds for starters.

In fact, it seems to already be a problem, with over 61 million acres as of 2012.

Those weeds didn't develop Round-Up resistance through GMO. They developed it through old-fashioned selective breeding. Self-selective, but still selective. The Round-Up resistance in the weeds would've happened whether the crops were GMO or not, so long as they were created with the Round-Up resistance one way or another.

Selective breeding is a lot more predictable than directly twiddling genes. There are a lot of unforeseen side-effects.

Such as?

As we've seen with antibiotic resistance, expect Round-Up resistant weeds for starters.

In fact, it seems to already be a problem, with over 61 million acres as of 2012.

Health-wise, GMOs seem to have proven themselves pretty safe - not the worse thing in our diets.

But not sure what most of them are really for. Leaving out Golden Rice, which is awesome, there isn't a food shortage that GMOs are trying to solve, there's a huge amount of wasted food:

The Food and Agriculture Organization (FAO) of the United Nations, which keeps tabs on what's grown and eaten around the globe, estimates that one-third of food produced for human consumption worldwide is annually lost or wasted along the chain that stretches from farms to processing plants, marketplaces, retailers, food-service operations, and our collective kitchens.

At 2.8 trillion pounds, that's enough sustenance to feed three billion people. In the United States, the waste is even more egregious: More than 30 percent of our food, valued at $162 billion annually, isn't eaten. Pile all that food on a football field and the layers would form a putrefying casserole miles high.

Anyway, for the most part I don't see the rush to GMOs, and I'm definitely in favour of labelling and can't understand anyone being against it other than for knee-jerk reasons. Let the market decide indeed.

and it is possible we are simply out of time, with regards to the funding for this sort of research.

That seems unlikely. The future is never as bleak as some would have you believe.
There have been a number of developments of late that suggest real progress is being made:

http://about.bnef.com/press-releases/cellulosic-ethanol-heads-for-cost-competitiveness-by-2016/
http://www.forbes.com/sites/christopherhelman/2013/09/04/same-moonshine-different-name-welcome-to-the-age-of-cellulosic-ethanol/

Somewhat dated:
http://www.nrel.gov/continuum/sustainable_transportation/cellulosic_ethanol.cfm

However, its still ethanol.
It may be wiser to take a look at other fuel stretchers as well.
Butanol is being looked at because it is less corrosive and also higher energy density than ethanol, almost approaching that of gasoline. (Exhaust smells like bananas).

Butanol trumps ethanol in several ways: Adding ethanol to gasoline reduces fuel mileage, but butanol packs almost as much energy as gas, meaning fewer fill-ups. Butanol also doesn't damage car engines like ethanol, so more of it can be blended into gas. And because butanol doesn't separate from gasoline in the presence of water, it can be blended right at the refinery, while ethanol has to be shipped separately from gas and blended closer to the filling station.

Even Zebra poop is helping, it yields a particular strain of Clostridium bacteria that can convert nearly any form of cellulose into butanol very efficiently.

Burned by itself, (B100) you might have a 10% mileage penalty. Mixed with gas it might not even impose any significant mileage penalty.
Its been found that the mileage penalty does not exactly vary in lock-step with energy density. (Theoretically ethanol should only see a 2 to 3% mileage penalty, but some claim 10%, especially on older vehicles). But to date, no one has done significant real world testing on Butanol + Gas blends.

Some links to Butanol stories:
http://tech.fortune.cnn.com/2013/04/12/the-fuel-that-could-be-the-end-of-ethanol/
http://farmindustrynews.com/blog/bio-butanol-can-be-produced-about-same-cost-ethanol-optinol-reports
http://www.acs.org/content/acs/en/pressroom/newsreleases/2013/april/cost-saving-measure-to-upgrade-ethanol-to-butanol-a-better-alternative-to-gasoline.html

Here is an article with a good snapshot of tractor automation as it currently exists in commercial implementations. It sounds pretty modest - a tractor pulling a grain cart autonomously follows alongside a combine. One vendor mentions safety, and none mention regulation as an issue.

I would be interesting if Monsanto was also working on insects/plants that can defeat their products as they come off of patent protection...

Of course nature is doing this already (for patent protected products), Roundup resistant weeds are spreading very quickly it appears (25% expansion in 2011, 51% in 2012, per the link):
http://farmindustrynews.com/herbicides/glyphosate-resistant-weed-problem-extends-more-species-more-farms

http://farmindustrynews.com/seed/0904_seed_university_prices/

Some of the fancier crap is at $350 now, so $500 is quite feasible. I know what we paid for a bag of seed corn in the 90's, and it was right around $50-$75. If you're really that interested, I could dig in our old files and probably find some of the handwritten seed bills we have and scan them in for you.

I'm getting sick of everyone PANICING that there will be no more plastics when oil is depleted or expensive. It's been known for a while now that plastic can be made from corn. See here: http://farmindustrynews.com/mag/farming_plastic_co rn/index.html
I have no insight as to how to replace other refinery byprodcuts. However, I'm sure someone will figure something out.

this article estimates manure cost at about $40/acre... not sure of the tonnage.