1.  How Clark said what he said:  It was said in the simple, direct prose of a life-time military officer.  No evasions, no dodging.  Similarly, as others have noted, he wouldn't have come out and said it and said it the way he did, had he not meant it and been prepared to stand behind it.
   
2.  What he said:  A couple things.  
   

(C)  The overlooked aspect in this is McCain's command - later.  He was a relatively undistinguished commander of a peacetime squadron.  He got that job as much as a reward for his having been a POW and for being the scion of a Navy kaderfamilie as anything else.  Despite the post hoc (and false) allegations he quit the Navy in spite of being selected for admiral (no way an undistinguished squadron commander would have gotten a flag), he rose to the level of his incompetence and a bit beyond - aided by his personal heroics.

But, digging in a little can be productive.

The easy comparison which pretty much everyone can understand is this - Ted Williams was one of the greatest baseball players ever, but his record as manager (of the Washington Senators, etc.) was mediocre at best.  Joe Maddon, OTOH, currently managing the Tampa Bay Rays, never played a single out in the Major Leagues and spent about 4 years in the minors, but his team is currently in first place in the AL East (Ahead of the Red Sox and Yankees).  

Great players, as a rule, do not make great managers.  Teddy couldn't relate to lesser-skilled players, nor get the most out of them, which is a (not the only) reason his managerial career was short and unsuccessful.  Mediocre players can - but don't necessarily do - make good managers.  
Pretty much the same obtains for politicians.

A baseball manager, in large part, selects who plays and has substantial input (it varies from team to team) into who is on the team in the first place.  A president has the same sort of selection of personnel.  And, remember, policy is personnel.

A squadron commander in the Navy, OTOH, pretty much has to take the people he's given and deal with that.

McCain never was a great squadron commander, and didn't do much with the resources he had.  Presently, McCain's selection of personnel belies his lack of experience in managing anything and wholesale lack of judgment.  He's surrounded by whatever hairballs (and heirballs) the Republican party has hacked up - and most of them are lobbyists, often for some of the most odious tyrants the world has seen.
One is compelled to wonder whether and to what extent McCain actually selected the campaign staff he has - as opposed to having it more-or-less presented to him ready to go.

Comparing Maddon of the Rays - he spent almost 30 years as a manager (and went to a near-Ivy college, too).  No dummy he, and no lack of experience in motivating and selecting personnel.  McCain, OTOH, has never exhibited the kind of discipline or insight a successful manager would.  He's what I call a "done 'fer" - everything's been done 'fer him and people have covered his errors, catastrophes and such first because he came from a prominent family and second because they saw they could ride his back to power and profit.

In other words, McCain is just like George W. Bush.  And in more ways than can be easily counted.