Yours is a valid point, but I think that there are really two different issues being conflated here.
The first is that Ars Magica skill ranges are relatively small compared to die roll ranges -- so it happens rather too often that someone who is definitely better at a skill (say, a score of 6 vs. a score of 3, or a score of 9 vs. a score of 6) gets beaten. Would your point still hold if Ars Magica rolled e.g. 1d2 instead of 1d10?
The second is indeed whether a "weak" character (in the area being tested, according to his mechanical description) should or should not manage to accomplish great things if played in a particularly brilliant way. Personally, I think he shouldn't! In fact, I think this is a fundamental limitation of many if not most rpgs: the character played by a "smart" or "charismatic" player gets an unfair advantage because that player often maneuvers him into a position of advantage -- whereas the ability of gaining such a position should already be encompassed by the skill involved. E.g. it's the good swordsman, not the character of the smart player who should occupy the chokepoint allowing him to take on his 20 enemies one at a time. Similarly, it's the character skilled in Charm/Intrigue who should think about getting the confidence of the king by getting first that of his wife/daughter/vizier, not the character of the smart player. Etc.
You are absolutely right, ezzelino, ability and characteristics have to count for something. I take a dim view of players trying to do end runs like this. If you want to play a combat machine don't think your RP skill will carry you through all your social interactions, ignoring those abilities.
My vague example was thinking of the player who has the abilities, is doing some inspired RP and the dice just aren't there for him. I've had nights like that, where I roll 2 or 3, or 4 the hard way, and I just need an average roll to succeed and can't find the average roll. And that is altogether different from botching.
As you point out, there's a lot of overlap with the other social abilities, and I don't like that, so I cut out Intrigue entirely (also charm, but that one required me to actually expand other social skills slightly).
I happen to like that overlap, and we interpret the use of social abilities very liberally. Basically we allow the player in question to choose which one he uses - providing he can explain why it would be appropriate - and the effect depends on the situation and ability used. And for great failures or Botches this is important.
Also, we require players to explain a little about how and what they do in this social situation, with good ideas reflecting positively on the situation.
As I read Intrigue in the core book it is as much about plotting and scheming as it is about negotiating and diplomacy. So when I use Intrigue I need to choose a tactic, whether to be sneaky and play both sides against each other, or to seek compromise.
"I try to talk to maga Lisandra and get her opinion on the issue before the tribunal."
Well, what ability to use? that depends on, and thus defines, your approach!
If you're trying to charm her, use Charm. If you're pretending something that is not true, Guile might be your key.
If you want the information, without her knowing that you've learned her opinion, Intrigue is definently the Ability to use.
So we let people decide what ability to use, and then let the scene resolve depending on that choice (and how well they've rolled).
Failing with Charm is very different from failing with Intrigue, for example.
The choice of Ability can be enhanced even further with how it is used. Charm for instance can be used to either flatter someone, to make them feel important and subsequently be helpful or reveal information. But I could also be used to draw attention to your own awesomenss and once impressed people may do your bidding. And so on.
If Magus A had Magus B so impressed with Magus A due to charm and started having Magus B do his bidding, I'd switch things to Leadership after the first request. It's obviously gone beyond being charming at that point.