So what are you doing about it? Ignoring it? Meeting his challenge head on? Sending him an email to get with him to show him why he is wrong? Whining about it? dismissing it or what?
I suspect most Aikidoka will dismiss it, for reasons he addresses very well in his article.
It would be fun to debate him on some minor points he may not have addressed already, but on balance he's correct enough that it wouldn't refute his central theme of the importance of aliveness if gaining real ability is your goal, although there is a bit of throwing the baby out with the bathwater and painting "traditional martial arts" with a broad negative brush.
He leaves himself an out by stating that anything shown to work will be incorporated in accordance with what is essentially the scientific method approach of JKD. One of the small problems with that position though is that *somebody* has to be doing the research a la the scientific method to see what else in the traditional arts can function "alive" in modern contexts. If he automatically paints everyone pursuing anything traditional as a de facto wanker then that can't happen and everyone has to assume that the current MMA blend can't be improved upon. There are certainly capable groups such as the Dog Brothers who are actively experimenting with incorporating kali/silat into the MMA context, and perhaps such efforts are more deserving of respect than what Thornton's position would seem to imply. It's not like kali/silat has never been used against live opponents, it's just that the live context was different than the MMA context.
Interestingly it appears that Ueshiba actively focused on creating counters to the judo syllabus back in the day, so it's not a stretch that he would continue to adapt if he were alive today. Without such active work to update Aikido, I think Thornton's criticism of it is particularly apt and biting (especially when it comes to the negative correlation of real ability and "dojo attitude" in Aikido vs what he refers to as "true" arts).
Then there is also the issue of "too deadly for the ring" techniques, which IMO has been addressed too broadly. While it can be, and often is, used as an excuse for low-percentage techniques, it *is* legitimate to observe that the fighting context shapes the optimal mix. If for example strikes to the back of the head were legal in MMA, it would change the safety equation of going for leg takedowns and the risk of being sprawled on to expose the back of the head and spine to strikes, and it would otherwise alter the optimal strategy and syllabus.
Related to this, and a finer point on the "too deadly or not" issue, is that one can look at the "percentage" of a technique (how likely it is to a) have an opportunity to use it come up, and b) how likely is that the attempt to use it will be successful) as a function of context as well. Let's take the straight blast itself as an example. Despite being in the name of SBGi, I don't know if they even train the straight blast or the boxing blast anymore, but clearly it's not something you see in MMA events. Presumably the reason for this is that it's vulnerable to a level change/leg attack or otherwise not considered to have a good risk/reward profile compared to other things. But how many people on "the street" would be expecting a straight blast? In other words Vunak's approach of intercept-straight blast-headbutt/knees/elbows could have a significantly higher percentage at the local bar than the MMA ring. You could think of it in terms of a financial investment where it doesn't risk much but might have a good reward if it's successful. In other words despite the fact that everyone would be on to you if you pulled it off in a single MMA match you would be investing in a certain probability of being able to end a fight very quickly instead of immediately resorting to a strategy with a "high percentage but potentially slow" profile. In MMA you can afford to grind out a win against a similarly-skilled opponent, whereas in a "real" situation a mixed strategy where you take a chance to win quickly by surprise and have a fallback strategy may be optimal. That doesn't take away from the need for alive training, but again there's a finer point to be put on these things than what he argues.
Another issue is that he seems to entirely deride the value of building a particular foundation in any art prior to applying real pressure. This is particularly pertinent to topics such as IS, where there is a considerable investment needed to learn a counterintuitive body coordination prior to going "live" and applying pressure. Obviously in modern times it's a fair criticism that a method that requires umpteen years of such training before you can do anything meaningful against increasing degrees of resistance isn't practical if you're looking to realize a reasonable level of usable skill let alone maximize your learning curve, but in any case there are reasons that the traditional arts evolved the way they did, and I think there is more to be mined there (for those interested of course). As he says, at the end of the day fighting skill isn't all that useful a thing, so frankly I think an approach of mining traditional arts for practical modern use a la the Dog Brothers is just a more interesting hobby than bashing it out at the local MMA gym with the currently approved decaffeinated sport blend.