http://breakingdefense.com/2014/04/navys-magnetic-super-gun-...
http://www.theguardian.com/us-news/2014/dec/10/us-navy-test-...
That still leaves the vulnerability of the new class of hypersonic anti-ship weapons systems, but I suspect there is something to attempt to counter that as well. The X-51A Waverider and any future versions are a good example of that.
This is all cat and mouse, but I wouldn't be so quick to completely discredit a carrier strike group. Yes the Carrier is a HUGE liability, but the amount of firepower in 1 group is simply mind numbing and taking out the entire group before a sustained counter attack would be near impossible. For reference, the US Navy currently has 10 of these operating globally.
If you recall, during the opening war in Afghanistan, a CSG managed to launch 1 Tomahawk cruise missile every 12 seconds for 48 hours sustained during the opening salvo. That is only a single CSG.
UAVs do not yet have the autonomous intelligence to operate on their own, and even if they do, we haven't yet decided to give robots the decision to kill autonomously.
Answer 2 =) we already do, to some degree. E.g., Cruise Missiles have had the ability to navigate on inertial guidance and terrain-following technology for decades, and we use those a lot. But again, a cruise missile can only get programmed for one target, go there, and hit it.
A pilot can go to the target area, notice that the target has moved or new conditions exist (e.g., a bunch of children have been moved in as human shields), or notice that new targets of opportunity have popped up, and immediately take appropriate action.
And, we're back to the autonomous AI tech is not yet that good (and I'm not sure that we want it to get that good).
The Block IV missiles can also share targets amongst eachother and decide which target to strike (among a list of programmed targets) themselves based on factors such as proximity and other classified bits.
http://gizmodo.com/this-tomahawk-is-a-mighty-morphin-cruise-...
That said, note that even your example included live updates via comms/satellite links...
Consider the scenario where comms and orbital assets are unavailable/unreliable.
We still need human pilots. We're working to the day when we won't, but, we're not there yet.
(BTW, I'm all for unmanned, and think the F35 is already obsolete, and that humans are the limiting performance factor in esp. fighter aircraft (e.g., limiting it to 10g accelerations, but we're just not there yet for all scenarios, to answer the GP question as to "why not")
Carriers seem to be highly effective in uncontested waters, allowing force projection anywhere in the world. The article is saying that carriers are becoming less relevant when contested by a prepared enemy.