There are certainly right and wrong ways of doing it.
I suppose it's worth pointing out the pertinent news of the last week, with EA saying they're going to start
including microtransactions on every game from now on, and CliffyB voicing up about it (yeah, I am going to use Eurogamer for my gaming links now).
What worries me is that when a company like EA creates a seemingly blanket policy for having a certain feature in every one of its games, then it drastically increases the chance of that feature being implemented in some of those games in a bad way, like what you've mentioned above.
I don't agree that microtransactions are the future. They're just part of the future, like tablets and phones haven't killed consoles and PCs, they've just added to the mix. And poorly made ones still don't sell well.