The only way microtransactions truly work, and by that I mean they don't wreck your game, is if the items on sale really ARE optional.
By this I mean that character power can't be directly tied to a microtransaction (I shouldn't be able to plop down $20 for Excalibur for instance). However, if I want a costume that makes me look like Santa Claus (and does nothing else), that can be a microtransaction without ruining anything. You'll find that the games that haven't destroyed themselves with their F2P model have operated similarly to this. Cash shop items are cosmetic.
Guild Wars 2 is a great example of this. Their cash shop has minimal impact on the game, about the only thing in there that has any affect on anything is the exp bonuses you expect to see in any cash shop, but really, it's not that big a deal with the way their questing works anyway.
When a game transitions from p2p to f2p, a lot of times they do it wrong and you end up with something soul crushing (hi, SWTOR). But it can absolutely be done right and save a game that would otherwise just be shut down (hi LOTRO and DDO). Making that change doesn't have to mean the game is a failure, it just means that the subscriber numbers aren't enough to keep it running by themselves.
Honestly, if MMO developers would please stop trying to be the next WoW-killer, and design themselves into a niche market that can be successful with a few hundred thousand subscribers (FFXI did this brilliantly), I think you'd see a lot fewer subscription games going free-to-play, and a lot more happy MMO players who can find games they enjoy playing.