ArenaNet simplified the exchange in a recent build, giving players preset options to buy gems with gold or sell gems for gold. However, as the lowest gem bundle price point is 400, it's irked players who wish to buy smaller increments for some of the cheaper options in the store and feel as though they're overbuying gems in these situations.
Forum Communications Team Lead Gaile Gray gave an explanation for the change and said that the team is evaluating feedback: "The goal was to make the gem store more like other shopping experiences, and if you think about it, there is more of that feel to it now. You may be surprised to know this (I know I was) but very few people bought gems at smaller denominations than the first one offered in the new system. That's not to say they never did, nor that there wouldn't be the desire to do so. But overall, the current options were selected based on player purchases in the past. The team is going to listen to your feedback and, if and when it's practical and desirable, they can look towards adjusting the new system to better meet your needs."
[Update: Gaile Gray has reassured players that ArenaNet will reverse course on GemGate. "In light of your feedback, we will update the Currency Exchange so that you can decide how you want to use it," she wrote on the official forums. "We will keep the new streamlined system and also offer a new 'Custom' button on the panel that you can use to exchange any increment of gems or gold. We anticipate rolling this out soon. Stay tuned!"]