That's horribly unreliable too because sometimes players only get to bat for one ball at the death whereas other times they'll have the opportunity to bat the whole 50. One innings =/ one innings.
Your criticisms of averages are all true though. I think we just have to admit that statistics aren't especially useful in ODIs, and when it comes to T20s there's not much point even keeping them. Because we're cricket people we're used to reeling out statistics a lot but outside of the test and first-class game they're really not very good measure at all.
Well, it is not free from the frailties of an average.
However I don't think it's horribly non reliable as well. Any statistical measure Will look meaningless with such a small sample size like 2 games. But let's extend your example to a few more games.
Suppose he made scores of 50, 2*, 5*, 15*, 6*, 2.... all this at a strike rate of 120. His average would be 40.
Now those are perfectly respectable figures, but then what is the 'real utility' the team is getting by carrying such a batsman? He's contributing the odd 'bail out' innings once in 6 innings or so, but overall is contribuing about 13 runs per innings at a relatively low strike rate. Unfortunately for him, he's coming in a bit too low the batting order and hence is redundant. The team can actually get in another bowler in his place.
Meanwhile I think a minimum number of balls faced to be include in the super average calculation as it will take care of extreme fluctuations in strike rate due to less number of balls faced particularly while batting in the top order. I think a top order batsman should face atleast 20 balls in a twenty twenty. So if he makes a 20 from 10 balls regularly, then his strike rate should be normalised by dividing with 20 and not 10, hence 100 and not 200. Suppose team strike rate is 125, them his super average would be 20 X 100/125 which is 16.
Of course if he's not out then the strike rate doesn't apply.
The minimum balls to be faced also could be prorata reduced according to the over in which the batsman comes in to bat.