It seems to me that the biggest complaint again gold and those that use a lot of it is that the advantages it gives are too large.
In my opinion, the use of gold represents a large advantage in grepolis, particularly in 2.0. The 2.0 farming system allows players to demand resources all day, whereas in 1.26 (or whatever you want to call the patch) eventually the mood of the one's farms became too low to loot further, and so one had to take a couple hours off from farming runs, or had to loot other player's cities for additional resources. In 1.26 this meant that players were limited on how much they could earn per day from farms; I think if you were clever about it you could potentially get around 88,000 resources per island per day (upon request, I can explain how I got this number). In 2.0, even with just 5 level 3 farms, one can get a potential of 87,500 resources per island per day. Now here's the kicker:
The administrator allows a larger building queue. If you're online 24 hours a day this doesn't make much of a difference, except that whereas with a 2 building queue you might overflow with resources, you can spend your extra resources on the extra 5 buildings you can queue up. However, if you are on and off the internet throughout the day the administrator enables you to have continuous building. Over the course of 3-4 weeks, even without farming the difference is notable (I've founded about 25-30 cities on lambda, they grew twice as fast with the use of the administrator). Moreover, the attack overview available with the administrator puts all of your orders in one place and makes it far easier to snipe attacks, line up attacks close to one another, and allows a player to quickly browse through all of their cities as soon as an attack comes online. Additionally, the other overviews allow players to quickly run festivals, fill caves, queue barracks and harbors and do all the other administrative stuff daily in far less time than players that don't use the administrator. The time that players save on doing these things frees up time for farming, among other things. Especially when players acquire over 40 cities, they can save a huge amount of time using the administrator.
Captain gives 20% extra strength to the navy. That's a big bonus, and noticeable. What is more important though, is that the captain allows players to farm all the farms on an island with one click. This actually saves quite a bit of time for players, especially when they have 3 or more cities. Specifically, I estimate players can cut down about 80% of the waiting for individual farms to load on the browser by using the captain (one click instead of 8!). Over the course of a day, with perhaps 120 demands per farm (perhaps 300!) this is actually a significant amount of time that premium players free up for themselves to commit to other things. And remember, with the 2.0 farming system players can potentially gain far more resources by farming than they ever could in grepolis 1.26. In reality, the players that don't use Captain to free up this time generally just end up farming less and have far fewer resources to devote to building their city and troops. In this way, grepolis awards players for activity-- but in a very extreme way.
Merchant gives 30% extra resources from the farm nodes. With fully built up cities, 30% extra resources translates to 30% extra troops (If you are constantly fighting other players and never completely fill your nukes). With farming, this the difference between players that use merchant and those that don't is somewhat less than this.
Commander gives 20% extra troop strength. Again, this is a noticeable difference. High Priestess gives extra favor; the only way I can see this being abused is the fact that aggressive players are able to buff 50% (on average) of their attacks, and have a much easier time running population growths and rebuilding myth nukes.
I believe other people have already commented on the advantages of being able to summon the Phoenecian Merchant.