It's true with Inconsistent, there doesn't seem to be a way you can be 100% guaranteed to beat it (in the same way that Magneton could almost flawlessly counter Skarmory in Generation III), but that goes with lots of things.
If we're not going down the "ban it because of evasion clause" route, I think we should go down the same route as we do with everything else that is broken, (i.e. nominate it, test it some more, discuss and debate, vote on it, etc.). There is the obvious question of "Where do we draw the line when banning abilities?", but this can be avoided if Inconsistent fits the criteria to be banned through the evasion clause, whatever they are.
I see the similarities with the Jirachi example, but we're talking about such minute probablities here. I mean, with Inconsistent, you'll be, on average, at +1 evasion after an average of 3.5 turns (if my maths is correct), and you'll raise your evasion by one stage on average every 7 turns, but like how much damage does Iron Head do to Magneton and Magnezone? Magneton has a sky-high Defense stat now, and Magnezone might heal most of Iron Head's damage off through Leftovers.