Actually, I think it makes sense that Dungeoneering has a cap of 120 and everything else has 99. Dungeoneering is a 'skill of skills', it's practically the final achievement in terms of training skills, so it makes sense that it goes a
little bita lot further. If you make other skills that are so much more of a grind have a cap at 120, Runescape has slipped much further towards the status of grindfest than it already has. I'd rather there was more content for more variety (but not faster) in terms of training methods than simply giving another ridiculously boring goal.
It's like something of all the skills added together, in a minigame-like-skill. The level 120 milestone is just a milestone.
I believe that 120 Dungeoneering is a sign that you actually mastered the game, from top to bottom. You're not forced to get 120, you're already a master at 99, 120 is optional.
That's seems like a very plausible reason why Jagex decided to put a lvl 120 in the game. Though i'm still waiting for the day people with 200M XP in a skill finally get some recognition.
They are so few, it would be a waste of time for Jagex to assign a team to recognize them. It's enough that they're ranked first (or on the first page) of their skill.