You do not have to pay 50 cents/3 dollars to reskin your armor or weapons.
What you pay for them are gems. It's one's choice to pay for gems with real money, but you can also buy gems with in-game currency, whose price fluctuates on supply/demand.
Every single time I see people whine about the microtransactions in GW2, they always ignore this. Whether or not it's because they never bothered to look at the 2nd tab of the Trading Post or if they have some sort of motivation to provide misinformation to their readers is up in the air, though.
A second problem with your conjecture of their expense is that the transmutation gems can be obtained by random drop via the daily achievement system, for free. I've played this game non-consistently over the last few months (I didn't play at all during January or February) and I've still managed to get a stack of about 60 1-79 basic transmutation gems and 20 lv.80 transmutation gems just sitting in my bank. Unless you do serious constant re-skinning or gear customization most players do not have to buy these stones with gems at all.
But I strongly suggest you should edit this article to reflect these facts, as this seems to be the crux of why you think this system needs to be fixed.
The Scrying Pool: Transmutation Woes
This edition of the Scrying Pool wonders if the transmutation system is all it could be.
Instead of a locker that would store gear, I would expand the transmutation system through a system similar to the Hall of Monuments.
The Hall of Monuments was a way to reward Guild Wars 1 players. After obtaining special titles or items, players would visit the Hall of Monuments to record their achievements. These would be tallied into points. The more points a player earned, the more items and titles were unlocked for the player in Guild Wars1.
Through the use of a portal stone, players in Guild Wars 2 could teleport to the Hall of Monuments where a merchant would sell any weapons or gear the player had unlocked. The merchant only shows items that are unlocked. Anything that was not unlocked simply would not show up in the merchant window.
This is how I would expand the transmutation system: a merchant that showed any weapon or gear that the player had already unlocked. How would players unlock weapons and gear? Through the use of a Transmutation Gem.
Originally this idea was to replace the current transmutation stones and crystals but, while the current system isn't perfect, it isn't bad in every case. Any player who wants to only have a single look for the rest of forever would benefit just fine with the current stone and crystal system.
Transmutation Gems are used at first in a very similar way to stones and crystals: the player uses the item and transmutation window opens up. Instead of having two slots, however, it will have just a single slot for a single item. Players would insert a piece of gear into this slot where it would not show any of the stats of applied upgrade but solely the name and icon of the item. This system only takes into consideration the appearance of an item to be transmuted. After the item is in players would click the Unlock Transmutation button at the bottom of the window (which would be greyed out if that skin has already been unlocked).
After a skin is unlocked it would be added to the list of skins available for purchase from a Transmutation Merchant. This merchant would likely have tabs for each type of equipment (Heavy, Medium, Light armor and each of the different weapon types) under which unlocked skins for that type of equipment would be shown.
Unlike the Hall of Monuments merchant, however, these skins would not be free. In addition to Transmutation Gems I would add Transmutation Shards to the game. Shards would essentially be currency similar to dungeon tokens that would be used to buy previously unlocked skins.
One of the problems I mentioned earlier with the current transmutation system is the cost to change appearances. With this system the Transmutation Gems would be bought through the gem store while Transmutation Shards would be obtained in game. The Transmutation Gems would be a one-time unlock for each skin while the Transmutation Shards would be used every time a player wanted to change his or her appearance.